Materials and Methods for Efficient Lactic Acid Production

ABSTRACT

The present invention provides derivatives of  Escherichia coli  constructed for the production of lactic acid. The transformed  E. coli  of the invention are prepared by deleting the genes that encode competing pathways followed by a growth-based selection for mutants with improved performance. These transformed  E. coli  are useful for providing an increased supply of lactic acid for use in food and industrial applications.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.11/501,137, filed Aug. 8, 2006, now U.S. Pat. No. 7,629,162, whichclaims the benefit of U.S. Provisional Application Ser. No. 60/706,887,filed Aug. 10, 2005; Ser. No. 60/761,576, filed Jan. 24, 2006; and Ser.No. 60/799,619, filed May 11, 2006. Each of these applications is herebyincorporated by reference in its entirety, including all figures andsequences.

GOVERNMENT SUPPORT

This invention was made with government support under a grant awardedfrom the Department of Energy under grant number USDOE-DE FG02-96ER20222and Department of Energy in conjunction with the United StatesDepartment of Agriculture under grant number USDA & DOE Biomass RDI DEFG36-04GO14019. This invention was also made with government supportfrom the U.S. Department of Agriculture under grant numbers01-35504-10669 and 00-52104-9704. The government has certain rights inthe invention.

BACKGROUND OF THE INVENTION

Lactic acid is commonly used as a food additive for preservation,flavor, and acidity. Lactic acid is also used in the manufacture ofbiodegradable plastic, namely polylactic acid (PLA). The use of PLA as arenewable alternative to petroleum-based products is rapidly expanding(Agrawal, 2003). Physical properties and rate of biological degradationof PLA can be controlled by manipulating the ratio of the chiralsubstrates, D-lactic acid and L-lactic acid (Narayanan et al., 2004).The global lactic acid market is estimated to be in excess of 100,000tons per year and is expected to increase substantially in the next fewyears as new PLA facilities become operational.

For example, demand for the biodegradable solvent ethyl lactate (aderivative of lactic acid) is expected to increase substantially in thenear future. It has been estimated that lactate esters could potentiallyreplace as much as 80% of the 3.8 million tons of solvents used eachyear in the U.S. This solvent is non-toxic and has many usefulapplications, including in electronic manufacturing, in paints andcoatings, in textiles, cleaners and degreasers, adhesives, printing, andde-inking.

Fermentative methods for production of lactic acid are often preferredover chemical synthesis, which results in a mixture of both D and Lisomers. The products of microbiological fermentations are dependent onthe organism used. Microbiological fermentation can yield a mixture ofthe two isomers or optically pure lactic acid in a stereospecific form.The desired stereospecificity of the product depends on the intendeduse.

Bacterial fermentations with Lactobacilli are common for industrialproduction of lactic acid, but these fermentations rarely yieldoptically pure product. Additionally, the fastidious nature of thesebacteria requires that considerable amounts of supplemental nutrients beadded to the growth medium, adding additional cost and makingpurification more difficult. Moreover, fermentation methods forproducing lactic acid are highly inefficient and must be improved toensure the economic feasibility of the aforementioned anticipated marketexpansions.

Yeast are not capable of producing appreciable levels of lactic acid,although recombinant Saccharomyces cerevisiae strains have beendescribed that contain the ldh gene from either Lactobacillus or bovineorigins (Patent WO 99/14335 and Adachi et al., 1998). While capable ofproducing up to 2-4% (w/v) lactic acid, these strains exhibit poorproductivity and a significant portion of the glucose is converted toethanol.

The filamentous fungus Rhizopus oryzae (syn. R. arrhizus) is also usedfor industrial production of lactic acid. R. oryzae is able toaerobically convert glucose, in a chemically defined medium, to largeamounts of optically pure L-(+)-lactic acid. Research on lactic acidproduction by Rhizopus has continued primarily because of the ease ofproduct purification in a minimal growth medium and the ability of thefungus to utilize both complex carbohydrates and pentose sugars (U.S.Pat. No. 4,963,486). This allows the fungus to be utilized forconversion of low value agricultural biomass to lactic acid.Unfortunately, the ability to modify lactic acid production by geneticmodification in Rhizopus and other fungi has been limited.

Escherichia coli K-12-based biocatalysts have been engineered forD-(−)-lactate production but were unable to ferment 10% glucose orsucrose to completion in complex or minimal medium (Chang et al., 1999;Dien et al., 2001; Zhou et al., 2003; Zhu and Shimizu 2004).

One of the E. coli biocatalysts, SZ63 (pLOI3501), was developed forsucrose fermentation by functionally expressing the cscR′ cscA′ cscKB′genes from E. coli B on a plasmid (Shukla et al. 2004). Although capableof efficient fermentation of 5% glucose or sucrose, higher sugarconcentrations were incompletely metabolized by this biocatalyst andcontinuous antibiotic selection was required for plasmid maintenance.

Other biocatalysts derived from E. coli strain B, such as K011 (DepositNo. ATCC 55124), have the native ability to ferment sucrose(Moniruzzaman et al., 1997). As with the strain SZ63, higher sugarconcentrations are incompletely metabolized by this biocatalyst andcontinuous antibiotic selection is required for plasmid maintenance.

Accordingly, a need still exists for improved lactic acid biocatalystswith increased fermentation rates, product titer, and yields to reducecosts associated with the bio-based production of commodity chemicals(Arntzen et al., 1999; Chotani et al., 2000; Datta et al., 1995;Hofvendahl and Hahn-Hagerdal, 2000; and Ohara et al., 2001).

BRIEF SUMMARY OF THE INVENTION

The subject invention provides novel microorganisms useful in theproduction of lactic acid. Additionally, the subject invention providesnovel constructs for use in transforming any of numerous host organisms,preferably Escherichia coli, to express and/or suppress certain genes toproduce lactic acid when the host organism is cultivated in afermentable medium. Accordingly, the materials and methods of thesubject invention can be used to enhance lactic acid production in hostorganisms thereby providing an increased supply of lactic acid for usein food and industrial applications.

In certain embodiments, derivatives of ethanologenic Escherichia coli(also referred to herein as E. coli) K011 are constructed for theproduction of D-(−)-lactate. In other embodiments of the invention, E.coli are engineered in accordance with the subject invention for theproduction of L-(+)-lactate.

In accordance with the subject invention, novel E. coli KOH-basedbiocatalysts are prepared by deleting the genes that encode competingpathways followed by a growth-based selection for mutants with improvedperformance for fermenting glucose and/or sucrose.

The engineered microbes of the invention preferably contain native genesfor sucrose utilization. Certain engineered E. coli strains of theinvention can ferment 10% glucose or sucrose to produce over 1 moleD-(−)-lactate/1 of fermentation broth, with yields based on metabolizedsugar ranging from about 88% to about 95%, depending on the fermentationbroth. Other engineered E. coli strains of the invention can fermentglucose or sucrose to produce L-(+)-lactate.

Additional advantages of this invention will become readily apparentfrom the ensuing description.

BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A-1F graphically illustrate the difference in activity between anembodiment of the invention as compared to strain SZ63. Symbols for FIG.1A: , SZ132 (lactate); ▴, SZ63 (lactate); ∘, SZ132 (cell mass); Δ, SZ63(cell mass). Symbols for FIG. 1B: , SZ132 (cell mass); ▴, SZ63 (cellmass); ∘, SZ132 (lactate); Δ, SZ63 (lactate). Symbols for FIG. 1C: ,SZ132 (lactate); ▴, SZ63 (lactate); ∘, SZ132 (cell mass); Δ, SZ63 (cellmass). Symbols for FIG. 1D: ∘, SZ63; , SZ132. Symbols for FIG. 1E: ∘,10% sucrose; , 5% sucrose. Symbols for FIG. 1F: ∘, 10% sucrose; , 5%sucrose.

FIGS. 2A-2D illustrate progress of lactic acid production by variousembodiments of the invention under fermentation conditions in NBSmineral salts medium.

FIGS. 3A-3B illustrate the ability of betaine to increase acid and sugartolerance during lactic acid production by one embodiment of theinvention.

FIGS. 4A-4B illustrate the ability of one embodiment of the invention toacclimatize to mineral media.

FIGS. 5A-5G illustrate progress of lactic acid production by yet anotherembodiment of the invention under various fermentation conditions.

FIG. 6 illustrates the metabolic evolution of SZ132 for improved growthand lactate production in 10% sucrose (pH 7.0). Strain SZ132 wassequentially transferred in mineral salts medium containing 10% (w/v)sucrose to enrich for spontaneous mutants with improved growth andlactate production without betaine. One clone, SZ186, was isolated fromthe final transfer. FIG. 6A shows cell mass. FIG. 6B shows total organicacids (base consumed).

FIG. 7 illustrates the metabolic evolution of SZ186 for improved growthand lactate production in 10% glucose (pH 7.0). Strain SZ186 wassequentially transferred in mineral salts medium containing 10% (w/v)glucose and 1 mM betaine to enrich for spontaneous mutants with improvedgrowth and lactate production. One clone, SZ186, was isolated from thefinal transfer. FIG. 7A shows cell mass. FIG. 7B shows total organicacids (base consumed to maintain pH).

FIG. 8 illustrates the comparison of lactate production by SZ194 inbatch and fed-batch fermentations. Fermentations were carried out inmineral salts medium containing 1 mM betaine (pH 7.5). FIG. 8A showssimple batch fermentation containing 12% (w/v) glucose; FIG. 8B showsfed-batch fermentation. Symbols for all: □, cell mass; , total organicacids (base consumed to maintain pH); ∘, glucose.

FIGS. 9A-9B show native pathways for lactate production in E. coli. FIG.9A is the Dihydroxyacetone-P node. FIG. 9B is the Methylglyoxal Bypass.Abbreviations: DHAP, dihydroxyacetone phosphate; Gly3P, glyceraldehyde3-phosphate.

FIGS. 10A-10F show fermentation of 12% (w/v) glucose (NBS mineral saltsmedium+1 mM betaine) to lactate by recombinant E. coli. FIG. 10A showsthe organic acid production by D-(−)-lactate strains. FIG. 10B shows thegrowth of D-(−)-lactate strains. Symbols for FIGS. 10A and 10B: Δ,SZ194; ∘, TG112 (10% w/v glucose); ⋄, TG113; □, TG114. FIG. 10C showsthe effect of mgsA deletion on organic acid production by L-(+)-lactatestrains (10% glucose+1 mM betaine). FIG. 10D shows the effect of mgsAdeletion on growth of L-(+)-lactate strains (10% glucose). Symbols forFIGS. 10C and 10D: , TG102 (mgsA⁺, 10% w/v glucose, no betaine); ∘, TG103 (mgsA⁺, 10% w/v glucose, no betaine); ▪, TG105 (mgsA deleted, 1 mMbetaine); *, TG103 (mgsA⁺, 1 mM betaine). FIG. 10E shows the organicacid production by L-(+)-lactate strains. FIG. 10F shows the growth ofL-(+)-lactate strains. Symbols for FIGS. 10E and 10F: ▪, TG105; ▪,TG106; ▴, TG107; ♦, TG108.

FIGS. 11A-11B show metabolic evolution for improved D-(−)-lactateproduction and growth. E. coli strain TG112 was sequentially transferredevery 24 or 48 hours in a mineral salts medium containing 10% or 12%(w/v) glucose and 1 mM betaine to select for spontaneous mutants withimproved growth, hardiness and lactate production. One clone, TG113, wasisolated as an intermediate from TG112 transfer number 28 (day 29) andanother clone, TG114, from the final culture on day 81. For clarity,graphs from every fourth 24-hour transfer and every other 48-hourtransfer are shown. The parent, SZ194, was included for comparison. FIG.11A shows the total organic acids (mM) calculated from base consumed tomaintain pH 7. FIG. 11B shows cell Mass (g/L). Symbols: ▴, SZ194, 12%(w/v) glucose; ∘, TG112, 10% (w/v) glucose, 1:100 dilution, 24 hourtransfers; , TG112, 12% (w/v) glucose, 1:100 dilution, 24 hourtransfers; □, TG113, 12% (w/v) glucose, 1:350 dilution, 24 hourtransfers; and ♦, TG113, 12% (w/v) glucose, 1:100 dilution, 48 hourtransfers.

FIGS. 12A-C illustrate the production of pLOI4417. pLOI4417 wasgenerated by performing PCR on pLOI4411 with a primer that annealed tothe 3′ end of frdA, extending upstream, and a primer that annealedwithin frdC, extending downstream (FIG. 12A). The resulting 4263 by PCRproduct was treated with restriction enzyme DpnI to digest the nativepLOI4411 plasmid (FIG. 12B). Digested PCR products were subsequentlyself-ligated in order to generate the new plasmid, pLOI4417 (FIG. 12C).

BRIEF DESCRIPTION OF THE SEQUENCES

SEQ ID NO:1 is the nucleotide sequence for a sense primer for frdBCdeletion.

SEQ ID NO:2 is the nucleotide sequence for an antisense primer for frdBCdeletion.

SEQ ID NO:3 is the nucleotide sequence for a sense primer for adhEdeletion.

SEQ ID NO:4 is the nucleotide sequence for an antisense primer for adhEdeletion.

SEQ ID NO:5 is the nucleotide sequence for a sense primer for celYdeletion.

SEQ ID NO:6 is the nucleotide sequence for an antisense primer for celYdeletion.

SEQ ID NO:7 is the nucleotide sequence for a sense primer for mgsAdeletion.

SEQ ID NO:8 is the nucleotide sequence for an antisense primer for mgsAdeletion.

SEQ ID NO:9 is the nucleotide sequence for a sense primer foramplification of FRT-cat-sacB.

SEQ ID NO:10 is the nucleotide sequence for an antisense primer foramplification of FRT-cat-sacB.

SEQ ID NO:11 is the nucleotide sequence for a sense primer foramplification of cat-sacB with 5′ NheI site.

SEQ ID NO:12 is the nucleotide sequence for an antisense primer foramplification of cat-sacB with 5′ NheI site.

SEQ ID NO:13 is the nucleotide sequence for a sense primer for cloningfrdABCD.

SEQ ID NO:14 is the nucleotide sequence for an antisense primer forcloning frdABCD.

SEQ ID NO:15 is the nucleotide sequence for a sense primer for cloningackA.

SEQ ID NO:16 is the nucleotide sequence for an antisense primer forcloning ackA.

SEQ ID NO:17 is the nucleotide sequence for a sense primer for cloninglacZ-cynX

SEQ ID NO:18 is the nucleotide sequence for an antisense primer forcloning lacZ-cynX.

SEQ ID NO:19 is the nucleotide sequence for a sense primer for cloningmgsA.

SEQ ID NO:20 is the nucleotide sequence for an antisense primer forcloning mgsA.

SEQ ID NO:21 is the nucleotide sequence for a sense primer for cloningfocA-pflB.

SEQ ID NO:22 is the nucleotide sequence for an antisense primer forcloning focA-pflB.

SEQ ID NO:23 is the nucleotide sequence for a sense primer for cloningadhE.

SEQ ID NO:24 is the nucleotide sequence for an antisense primer forcloning adhE.

SEQ ID NO:25 is the nucleotide sequence for a sense primer for deletingfrdBC.

SEQ ID NO:26 is the nucleotide sequence for an antisense primer fordeleting frdBC.

SEQ ID NO:27 is the nucleotide sequence for a sense primer for deletingackA.

SEQ ID NO:28 is the nucleotide sequence for an antisense primer fordeleting ackA.

SEQ ID NO:29 is the nucleotide sequence for a lacZ antisense primer with5′ NheI site.

SEQ ID NO:30 is the nucleotide sequence for a cynX antisense primer with5′ NheI site.

SEQ ID NO:31 is the nucleotide sequence for a sense primer for deletingmgsA.

SEQ ID NO:32 is the nucleotide sequence for an antisense primer fordeleting mgsA. SEQ ID NO:33 is the nucleotide sequence for a senseprimer for deleting focA-pflB.

SEQ ID NO:34 is the nucleotide sequence for an antisense primer fordeleting focA-pflB.

SEQ ID NO:35 is the nucleotide sequence for a sense primer for deletingadhE.

SEQ ID NO:36 is the nucleotide sequence for an antisense primer fordeleting adhE.

SEQ ID NOs:37-46 depict the partial sequence of the genetic regions inwhich FRT scars were deleted. Partial sequences of the 5′ and 3′ regionof the gene(s) are shown in bold, italics are used to designate the FRTscar and the underlined region was deleted in strain TG128.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides novel microorganisms that are capable ofproducing lactic acid when grown in a variety of fermentationconditions. The present invention also provides methods for engineeringsuch microorganisms as well as methods for efficiently and stablyproducing lactic acid using the novel microbes of the invention, so thata high yield of lactic acid is provided from relatively inexpensive rawproducts such as glucose or sucrose.

The term “lactic acid” in this application refers to 2-hydroxypropionicacid in either the free acid or salt form. The salt form of lactic acidis referred to as “lactate” regardless of the neutralizing agent, i.e.,calcium carbonate or ammonium hydroxide. As referred to herein, lacticacid can refer to either stereoisomeric form of lactic acid(L-(+)-lactic acid or D-(−)-lactic acid). The term lactate can refer toeither stereoisomeric form of lactate (L-(+)-lactate or D-(−)-lactate).The present invention provides microbes that produce a singlestereoisomer of lactic acid or lactate. The lactic acid stereoisomer orlactate stereoisomer that is produced in accordance with some aspects ofthis invention is “chirally pure”. The phrase “chirally pure” indicatesthat there is no detectable contamination of one stereoisomeric form oflactic acid or lactate with the other stereoisomeric form (the chiralpurity of the specified stereoisomer is at least, greater than (orgreater than or equal to) 99.9%). Genetically modified microorganismsdisclosed herein that have had the methylglyoxal pathway (mgsA) deletedor inactivated are able to produce “chirally pure” D-(−)-lactic acid orL-(+)-lactic acid.

For certain embodiments of the invention, L-(+)-lactic acid is producedusing the engineered microbes of the invention. In other embodiments ofthe invention, D-(−)-lactic acid is produced using the engineeredmicrobes of the invention.

In one embodiment, the invention uses Escherichia coli (or E. coli) as abiocatalyst for the enhanced conversion of glucose and/or sucrose tolactic acid. In accordance with the present invention, the metabolism ofa microorganism can be modified by introducing and expressing variousgenes. In accordance with the subject invention, various novel plasmidscan be introduced into E. coli so that the transformed microorganism canproduce large quantities of lactic acid in various fermentationconditions. The recombinant E. coli of the invention are preferablymodified so that lactic acid is stably produced with high yield whengrown on a medium comprising glucose and/or sucrose.

E. coli hosts containing the plasmids of the subject invention weredeposited with the Agricultural Research Service Culture Collection,1815 N. University Street, Peoria, Ill., 61604 U.S.A. The accessionnumbers and deposit dates are as follows:

Culture Accession number Deposit date SZ132 NRRL B-30861 Aug. 3, 2005SZ186 NRRL B-30862 Aug. 3, 2005 SZ194 NRRL B-30863 Aug. 3, 2005 TG103NRRL B-30864 Aug. 9, 2005 TG102 NRRL B-30921 May 5, 2006 TG105 NRRLB-30922 May 5, 2006 TG106 NRRL B-30923 May 5, 2006 TG107 NRRL B-30924May 5, 2006 TG108 NRRL B-30925 May 5, 2006 TG112 NRRL B-30926 May 5,2006 TG113 NRRL B-30927 May 5, 2006 TG114 NRRL B-30928 May 5, 2006 TG128NRRL B-30962 Jul. 25, 2006 TG129 NRRL B-30963 Jul. 25, 2006 TG130 NRRLB-30964 Jul. 25, 2006

The subject cultures have been deposited under conditions that assurethat access to the cultures will be available during the pendency ofthis patent application to one determined by the Commissioner of Patentsand Trademarks to be entitled thereto under 37 CFR 1.14 and 35 USC 122.The deposits are available as required by foreign patent laws incountries wherein counterparts of the subject application, or itsprogeny, are filed. However, it should be understood that theavailability of the deposits does not constitute a license to practicethe subject invention in derogation of patent rights granted bygovernmental action.

Further, the subject culture deposits will be stored and made availableto the public in accord with the provisions of the Budapest Treaty forthe Deposit of Microorganisms, i.e., they will be stored with all thecare necessary to keep them viable and uncontaminated for a period of atleast five years after the most recent request for the furnishing of asample of the deposits, and in any case, for a period of at least 30(thirty) years after the date of deposit or for the enforceable life ofany patent which may issue disclosing the cultures. The depositoracknowledges the duty to replace the deposits should the depository beunable to furnish a sample when requested, due to the condition of thedeposits. All restrictions on the availability to the public of thesubject culture deposits will be irrevocably removed upon the grantingof a patent disclosing them.

One embodiment of the present invention provides an E. coli B strain(“SZ132”; Deposit No. NRRL B-30861) that is engineered to enhance cellgrowth and lactate production in various media. In one embodiment, theSZ132 strain can be constructed to produce D-lactate (lactic acid) viathe following steps:

(a) constructing strain LY52 from E. coli K011 by integrating theKlebsiella oxytoca (Deposit No. ATCC 68564) casAB genes for cellobioseutilization behind the stop codon of lacY and integrating the Erwiniachysanthem (Deposit No. ATCC 55124) celY gene encoding endoglucanaseinto the frdA gene (Ohta et al., 1991; Moniruzzaman et al., 1997; Zhouand Ingram, 1999);

(b) sequentially transducing into LY52 certain mutations in E. coli K-12(strain W3110), which were used to construct the strain SZ63 (Zhou etal., 2003);

(c) eliminating Z. mobilis genes for ethanol production by P1transduction of the ΔfocA-pflB deletion from strain SZ31 (strain W3110);

(d) inactivating native E. coli alcohol dehydrogenase production by P1transduction of the adhE mutation from strain TC20 (Zhou et al., 2003);

(e) deleting acetate kinase (ackA) using the mutation from strain SZ61(strain W3110) (Zhou et al., 2003);

(f) removing antibiotic genes, which were used for selection, by FLPrecombinase (Zhou et al., 2003); and

(g) during removal of antibiotic genes of step (f), deleting an internalsegment of casAB (or deleting an internal segment of the casAB geneafter the step of removing antibiotic genes).

Related embodiments of the invention further involve transforming strainSZ132 to remove all foreign genes. In one embodiment, the Klebsiellaoxytoca casAB and Erwinia chrysanthemi celY genes were deleted fromstrain SZ132 by homologous recombination using linear DNA; then FLPrecombinase was used to eliminate antibiotic genes used duringconstruction of strain SZ132. The resulting strain, SZ186 (Deposit No.NRRL B-30862), contains only native E. coli genes.

Another embodiment of the present invention provides an E. coli B strain(“TG103”) that is engineered to enhance cell growth and the productionof the L isomer of lactic acid in various media. In one embodiment, theTG103 strain can be constructed via the following steps:

(a) engineering strain SZ186 using methods as described herein;

(b) subjecting strain SZ186 to serial cultivation to select forincreased growth and/or increased lactic acid production, wherein theselected strains are strain SZ194;

(c) integrating a heterologous L-lactic acid gene and kanamycin markerinto the native ldhA (D-lactate dehydrogenase) gene of SZ194 anddeleting the central part of the coding region to produce TG101;

(d) removing antibiotic genes by FLP recombinase to produce TG102; and

(e) subjecting strain TG102 to serial transfer for several days (such asfrom about 7 to 21 days, preferably for 13 days), with 1:100 dilution ofbroth from previously inoculated culture each day and selecting strainsthat demonstrate improved growth and/or increased L-lactic acidproduction, wherein the selected strains are TG103.

According to certain embodiments of the subject invention, increasedgrowth and increased lactic acid production are linked. The co-selectionprocess for strains with improved growth and lactic acid production isreferred to as “Metabolic Evolution.” Certain embodiments of theinvention also provide for the inactivation or deletion of certain geneswithin the genetically modified organisms provided by this application.In one aspect of the invention, the genes are deleted in order toinactivate the desired activity. Deletions provide maximum stabilitybecause there is no opportunity for a reverse mutation to restorefunction. Alternatively, genes can be inactivated by insertion ofnucleic acid sequences that disrupt the function and/or expression ofthe gene (e.g., P1 transduction or other methods known in the art). Theinactivation or deletion of one or more particular polynucleotidesequence as discussed herein can also be referred to as genetic“modifications.”

The vector used for introducing specific genes into a host microorganismmay be any vector so long as it can replicate in the host microorganism.Vectors of the present invention can be operable as cloning vectors orexpression vectors in the selected host cell. Numerous vectors are knownto practitioners skilled in the art, and selection of an appropriatevector and host cell is a matter of choice. The vectors may, forexample, be bacteriophage, plasmids, viruses, or hybrids thereof, suchas those described in Maniatis et al., 1989; Ausubel et al., 1995;Miller, J. H., 1992; Sambrook and Russell, 2001. Further, the vectors ofthe invention may be non-fusion vectors or fusion vectors.

Within each specific vector, various sites may be selected for insertionof a nucleotide sequence of interest. These sites are usually designatedby the restriction enzyme or endonuclease that cuts them. The vector canbe digested with a restriction enzyme matching the terminal sequence ofthe gene and the sequences can be ligated. The ligation is usuallyattained by using a ligase such as T4 DNA ligase.

The particular site chosen for insertion of the selected nucleotidefragment into the vector to form a recombinant vector is determined by avariety of factors. These include size and structure of the polypeptideto be expressed, susceptibility of the desired polypeptide to enzymaticdegradation by the host cell components and contamination by itsproteins, expression characteristics such as the location of start andstop codons, and other factors recognized by those of skill in the art.None of these factors alone absolutely controls the choice of insertionsite for a particular polypeptide. Rather, the site chosen reflects abalance of these factors, and not all sites may be equally effective fora given protein.

A variety of vector-host cell expression systems may be employed inpracticing the present invention. Strains of bacteria, such as E. coli,are particularly useful in producing lactic acid in the practice of theinvention. However, the novel invention described here can be appliedwith numerous hosts that would be desirable for various lactic acidproducing schemes. Host strains may be of bacterial, fungal, or yeastorigin. Factors that can be considered in choosing host strains includesubstrate range, hardiness, sugar tolerance, salt tolerance, temperaturetolerance, pH tolerance, and lactate tolerance. Ascertaining the mostappropriate host-vector system is within the skill of the person in theart.

Methods for chromosomal deletions, integration, and removable antibioticresistance genes have been previously described (Causey et al., 2004;Datsenko and Wanner, 2000; Martinez-Morales et al., 1999; Zhou et al.,2003). Any one or combination of such known methods may be employed inpracticing the present invention.

As the promoter for the expression of the gene(s) to be presented in thehost microorganism (for example, K. oxytoca casAB or E. chrysanthemicelY genes), when a promoter specific for the gene functions in hostcells, this promoter can be used. Alternatively, it is also possible toligate a foreign promoter to a DNA encoding the gene so as to obtain theexpression under the control of the promoter. As such a promoter, whenan Escherichia bacterium is used as the host, lac promoter, trppromoter, trc promoter, tac promoter, P_(R) promoter and P_(L) promoterof lambda phage, tet promoter, amyE promoter, spac promoter and so forthcan be used. Further, it is also possible to use an expression vectorcontaining a promoter like pUC19, and insert a DNA fragment, encodingfor example K. oxytoca casAB, into the vector so that the fragment canbe expressed under the control of the promoter.

Methods for preparation of chromosome DNA, PCR, preparation of plasmidDNA, digestion and ligation of DNA, transformation, design and synthesisof oligonucleotides used as primers and so forth may be usual ones wellknown to those skilled in the art. Such methods are described in, forexample, Sambrook, J. et al. (1989) and so forth.

Lactic acid can be produced by allowing a transformed microorganism, asdescribed above, to convert glucose and/or sucrose into lactic acid, andcollecting the produced lactic acid. In one aspect of the invention,lactic acid can be produced at levels of greater than 0.5M whentransformed organisms are cultured in a mineral salts medium, such asNBS mineral salts medium.

The vectors of the invention may be replicated autonomously orintegrated into the genome of the host. Integration typically occurs byhomologous recombination (for example, arginine selectable markerintegrating in the chromosomal arginine gene) or at a chromosomal siteunrelated to any genes on the vector. Integration may occur by either asingle or double cross-over event. It is also possible to have anynumber of these integration and replication types occurring in the sameconstructed microorganism.

In certain embodiments, cultivation of the engineered microorganisms ofthe invention is carried out under aerobic condition for about 0.5 to240 hours. The cultivation temperature is preferably controlled at about25° C. to 45° C., and pH is preferably controlled at 5-8 duringcultivation. Inorganic or organic, acidic, or alkaline substances aswell as ammonia gas or the like can be used for pH adjustment.

The microorganism of the present invention can be obtained bytransforming a bacterium belonging to Escherichia to express certainenzymes useful in the production of lactic acid. In a preferredembodiment, a bacterium belonging to Escherichia that can be used in thepresent invention is Escherichia coli.

In other embodiments of the invention, bacterium that can be used in thepresent invention include, but are not limited to, Gluconobacteroxydans, Gluconobacter asaii, Achromobacter delmarvae, Achromobacterviscosus, Achromobacter lacticum, Agrobacterium tumefaciens,Agrobacterium radiobacter, Alcaligenes faecalis, Arthrobacter citreus,Arthrobacter tumescens, Arthrobacter paraffineus, Arthrobacterhydrocarboglutamicus, Arthrobacter oxydans, Aureobacterium saperdae,Azotobacter indicus, Brevibacterium ammoniagenes, divaricatum,Brevibacterium lactofermentum, Brevibacterium flavum, Brevibacteriumglobosum, Brevibacterium fuscum, Brevibacterium ketoglutamicum,Brevibacterium helcolum, Brevibacterium pusillum, Brevibacteriumtestaceum, Brevibacterium roseum, Brevibacterium immariophilium,Brevibacterium linens, Brevibacterium protopharmiae, Corynebacteriumacetophilum, Corynebacterium glutamicum, Corynebacterium callunae,Corynebacterium acetoacidophilum, Corynebacterium acetoglutamicum,Enterobacter aerogenes, Erwinia amylovora, Erwinia carotovora, Erwiniaherbicola, Erwinia chrysanthemi, Flavobacterium peregrinum,Flavobacterium fucatum, Flavobacterium aurantinum, Flavobacteriumrhenanum, Flavobacterium sewanense, Flavobacterium breve, Flavobacteriummeningosepticum, Micrococcus sp. CCM825, Morganella morganii, Nocardiaopaca, Nocardia rugosa, Planococcus eucinatus, Proteus rettgeri,Propionibacterium shermanii, Pseudomonas synxantha, Pseudomonasazotoformans, Pseudomonas fluorescens, Pseudomonas ovalis, Pseudomonasstutzeri, Pseudomonas acidovolans, Pseudomonas mucidolens, Pseudomonastestosteroni, Pseudomonas aeruginosa, Rhodococcus erythropolis,Rhodococcus rhodochrous, Rhodococcus sp. ATCC 15592, Rhodococcus sp.ATCC 19070, Sporosarcina ureae, Staphylococcus aureus, Vibriometschnikovii, Vibrio tyrogenes, Actinomadura madurae, Actinomycesviolaceochromogenes, Kitasatosporia parulosa, Streptomyces coelicolor,Streptomyces flavelus, Streptomyces griseolus, Streptomyces lividans,Streptomyces olivaceus, Streptomyces tanashiensis, Streptomycesvirginiae, Streptomyces antibioticus, Streptomyces cacaoi, Streptomyceslavendulae, Streptomyces viridochromogenes, Aeromonas salmonicida,Bacillus pumilus, Bacillus circulans, Bacillus thiaminolyticus,Escherichia freundii, Microbacterium ammoniaphilum, Serratia marcescens,Salmonella typhimurium, Salmonella schottmulleri, Xanthomonas citri andso forth.

Lactic acid can be produced in a reaction mixture by contacting aculture containing transformed microorganisms prepared in accordancewith the present invention with sucrose and/or glucose. In otherembodiments of the invention, cells are separated and collected from aculture of transformed microorganisms; processed transformedmicroorganism cells subjected to acetone treatment or lyophillization; acell free extract prepared from such transformed microorganism cells orprocessed cells; fractions such as membrane fractions fractioned fromsuch cell free extract; or immobilized materials can be produced byimmobilizing transformed microorganism cells, processed cells, cell freeextract and fractions, any of which independently or combined contactedwith sucrose and/or glucose to produce lactic acid. The microorganismcan consist of one kind of microorganism, or can be used as an arbitrarymixture of two or more kinds of microorganisms.

Fermentation parameters are dependent on the type of host organism usedfor production of the recombinant enzyme. Growth medium may beminimal/defined or complete/complex. Fermentable carbon sources couldinclude hexose and pentose sugars, starch, cellulose, xylan,oligosaccharides, and combinations thereof. One form of growth mediathat can be used in accordance with the subject invention includesmodified Luria-Bertani (LB) broth (with 10 g Difco tryptone, 5 g Difcoyeast extract, and 5 g sodium chloride per liter) as described by MillerJ. H. (1992). In other embodiments of the invention, cultures ofconstructed strains of the invention can be grown in NBS mineral saltsmedium (as described by Causey et al., 2004) and supplemented with 2% to20% sugar (w/v) or either 5% or 10% sugar (glucose or sucrose). Themicroorganisms can be grown in or on NBS mineral salts medium. NBSmineral salts medium comprises, consists essentially of, or consists ofthe following components (per liter): 3.5 g of KH₂PO₄; 5.0 g of K₂HPO₄;3.5 g of (NH₄)₂HPO₄; 0.25 g of MgSO₄.7H₂O; 15 mg CaCl₂.2H₂O; 0.5 mg ofthiamine; and 1 ml of trace metal stock, glucose (e.g., 2% in plates or3% in broth), and 1.5% agar (for plates). The trace metal stock isprepared in prepared in 0.1 M HCl and comprises, consists essentially ofor consists of (per liter): 1.6 g of FeCl₃; 0.2 g of CoCl₂.6H₂O; 0.1 gof CuCl₂; 0.2 g of ZnCl₂.4H2O; 0.2 g of NaMoO₄; 0.05 g ofH₃BO₃.4-Morpholinopropanesulfonic acid (0.1 M, pH 7.1) can be added toboth liquid and solid media (filter-sterilized) when needed for pHcontrol (and is optionally included in medium used for 10-literfermentations). Minimal medium can also be prepared by using succinate(1 g·liter⁻¹) as a sole source of carbon (nonfermentable substrate) andcan be added as a supplement to glucose-minimal medium when needed. Incertain embodiments, antibiotics can be included as needed for strainconstruction.

Growth and production of the lactate can be performed in normal batchfermentations, fed-batch fermentations or continuous fermentations. Incertain embodiments, it is desirable to perform fermentations underreduced oxygen or anaerobic conditions for certain hosts. In otherembodiments, lactate production can be performed with oxygen; and,optionally with the use of air-lift or equivalent fermentors.

The pH of the fermentation should be sufficiently high enough to allowgrowth and lactate production by the host. Adjusting the pH of thefermentation broth may be performed using neutralizing agents such ascalcium carbonate or hydroxides. Alternatively, lactic acid can beremoved continuously during the fermentation using methods such asmembrane technology, electro-dialysis, solvent extraction, and absorbentresins. The selection and incorporation of any of the above fermentativemethods is highly dependent on the host strain and the preferreddownstream process.

Various non-limiting embodiments of the subject invention include:

1. A genetically modified E. coli strain that comprises the followinggenetic modifications to E. coli strain K011 (ATCC 55124): a) insertionof the Klebsiella oxytoca casAB gene behind the stop codon of lacY; b)integration of the Erwinia chrysanthemi celY gene into the frdA gene; c)inactivation or deletion of focA-Z. mobilis pdc-adhB-pflB; d)inactivation or deletion of the native E. coli alcohol dehydrogenasegene; and e) inactivation or deletion of the acetate kinase (ackA) gene;

2. The genetically modified E. coli strain according to embodiment 1,wherein said genetically modified E. coli strain further comprisesinactivated or deleted antibiotic resistance genes;

3. The genetically modified E. coli strain according to embodiment 1,wherein the Klebsiella oxytoca casAB gene and the Erwinia chrysanthemicelY gene are inactivated or deleted in said genetically modified E.coli strain after insertion;

4. The genetically modified E. coli strain according to embodiment 2,wherein the Klebsiella oxytoca casAB gene and the Erwinia chrysanthemicelY gene are inactivated or deleted in said genetically modified E.coli strain after insertion;

5. The genetically modified E. coli strain according to embodiment 2,wherein said genetically modified E. coli strain is metabolicallyevolved;

6. The genetically modified E. coli strain according to embodiment 1 orembodiment 3, wherein said genetically modified E. coli strain ismetabolically evolved;

7. The genetically modified E. coli strain according to embodiment 4,wherein said genetically modified E. coli strain is metabolicallyevolved;

8. The genetically modified E. coli strain according to embodiments 1,2, 3, 4, 5, 6, or 7, wherein the antibiotic genes are deleted with FLPrecombinase;

9. The genetically modified E. coli strain according to embodiment 7,wherein said genetically modified E. coli strain is SZ186;

10. The genetically modified E. coli strain according to embodiment 5,wherein said genetically modified E. coli strain is SZ132;

11. The genetically modified E. coli strain according to embodiment 1,2, 3, 4 or 5, wherein the mgsA gene of said strain is inactivated ordeleted in said genetically modified E. coli strain;

12. A genetically modified E. coli strain comprising E. coli strainSZ194 (NRRL B30863) in which the mgsA gene has been inactivated ordeleted;

13. The genetically modified E. coli strain according to embodiment 12,wherein said genetically modified E. coli strain is metabolicallyevolved;

14. The genetically modified E. coli strain according to embodiment 13,wherein said genetically modified E. coli strain is TG112, TG113 orTG114;

15. The genetically modified E. coli strain according to embodiment 11or 12, wherein said genetically modified E. coli strain furthercomprises an inactivated or deleted native ldhA gene and a recombinantlyinserted heterologous gene encoding an L-specific lactate dehydrogenase;

16. The genetically modified E. coli strain according to embodiment 15,wherein said heterologous L-specific lactate dehydrogenase gene is aldhL gene (for example, a ldhL gene obtained from P. acidilactici);

17. The genetically modified E. coli strain according to embodiment 15or embodiment 16, wherein said strain is metabolically evolved;

18. A genetically modified E. coli strain selected from TG112, TG113 orTG114, SZ194, SZ132, SZ186, or TG103;

19. A method of culturing or growing a genetically modified E. colistrain comprising inoculating a culture medium with one or moregenetically modified E. coli strain according to any one of embodiments1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17 or 18 andculturing or growing said a genetically modified E. coli strain;

20. A method of producing D-(−)-lactate or D-(−)-lactic acid comprisingculturing one or more genetically modified E. coli strain according toany one of embodiments 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or 14under conditions that allow for the production of D-(−)-lactic acid andoptionally neutralizing the D-(−)-lactic acid to form D-(−)-lactate;

21. The method according to embodiment 20, wherein said one or moregenetically modified E. coli strain is selected from TG112, TG113, TG114or SZ194;

22. A method of producing L-(+)-lactate or L-(+)-lactic acid comprisingculturing one or more genetically modified E. coli strain according toany one of embodiments 15, 16 or 17 under conditions that allow for theproduction of L-(+)-lactic acid and optionally neutralizing theL-(+)-lactic acid to form L-(+)-lactate;

23. The method according to embodiment 22, wherein said one or moregenetically modified E. coli strain is TG103, TG105, TG106, TG107, orTG108;

24. The method according to any one of embodiments 19, 20, 21, 22, or23, wherein said genetically modified E. coli strain is cultured in amineral salts medium;

25. The method according to embodiment 24, wherein the mineral saltsmedium comprises between 2% and 20% (w/v) of a sugar;

26. The method according to embodiment 25, wherein the mineral saltsmedium contains 2%, 2.5%, 3%, 3.5%, 4%, 4.5%, 5%, 5.5%, 6%, 6.5%, 7%,7.5%, 8%, 8.5%, 9%, 9.5%, 10%, 10.5%, 11%, 11.5%, 12%, 12.5%, 13%,13.5%, 14%, 14.5%, 15%, 15.5%, 16%, 16.5%, 17%, 17.5%, 18%, 18.5%, 19%,19.5% or 20% (w/v) of a sugar;

27. The method according to embodiment 25 or 26, wherein the sugar isglucose or sucrose or a combination of glucose and sucrose;

28. The method according to embodiment 20, wherein a geneticallymodified E. coli strain as set forth in embodiment 11 is cultured underconditions that allow for the production of chirally pure D-(−)-lactateor D-(−)-lactic acid;

29. The method according to embodiment 22, wherein a geneticallymodified E. coli strain as set forth in embodiment 15, 16 or 17 iscultured under conditions that allow for the production of chirally pureL-(+)-lactate or L-(+)-lactic acid;

30. The method according to embodiment 21, wherein said method produceschirally pure D-(−)-lactate or D-(−)-lactic acid;

31. The method according to embodiment 23, wherein said method produceschirally pure L-(+)-lactate or L-(+)-lactic acid;

32. The method according to embodiment 28, 29, 30 or 31, furthercomprising the step of purifying the chirally pure lactate(L-(+)-lactate or D-(−)-lactate);

33. The method according to any one of embodiment 20, 21, 22, 23, 24,25, 26, 27, 28, 29, 30, 31 or 32, wherein lactate (e.g., theL-(+)-lactate or D-(−)-lactate) is produced at concentrations of atleast 0.5M;

34. The method according to embodiment 33, wherein the culture medium isa chemically defined mineral salts medium such as NBS mineral saltsmedium;

35. The method according to embodiment 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33 or 34, wherein the yield of lactic acid(L-(+)-lactic acid or D-(−)-lactic acid) is at least or greater than (orgreater than or equal to) 90%;

36. The method according to embodiment 35, wherein the yield is at least90%, 90.5%, 91%, 91.5%, 92%, 92.5%, 93%, 93.5%, 94%, 94.5%, 95%, 95.5%,96%, 96.5%, 97%, 97.5%, 98%, 98.5%, or 99%;

37. The method according to embodiment 29, 30, 31, 32, 33, 34, 35 or 36,wherein there is no detectable contamination of one stereoisomeric formof lactic acid or lactate with the other stereoisomeric form (e.g., thechiral purity of the specified stereoisomer is at least, greater than(or greater than or equal to) 99.9%); or

38. A composition comprising one or more genetically modified E. colistrain according to any one of embodiments 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17 or 18 and medium.

Following are examples that illustrate procedures for practicing theinvention. These examples should not be construed as limiting. Allpercentages are by weight and all solvent mixture proportions are byvolume unless otherwise noted.

Example 1 Preparation and Analysis of E. Coli Strains SZ132 and SZ186

E. coli strains used in this Example are listed in Table 1. Strain SZ63is a derivative of E. coli K-12 (ATCC 27325). KO11 (ATCC 55124) is aderivative of E. coli B (ATCC 11303) that contains the Zymomonas mobilisethanol production genes integrated into the pflB gene.

TABLE 1 E. coli strains Strains Relevant Characteristics Sources DH5αΔlacZ M15 recA Invitrogen S17-1 thi pro recA hsdR RP4-2-tet::Mu Simon etal. 1983 aphA::Tn7 λpir TC20 ΔadhE::FRT-tet-FRT Zhou et al. 2003 SZ31W3110, Δ(focA-pflB)::FRT-kan-FRT Zhou et al. 2003 SZ61 W3110,ΔackA::FRT-tet-FRT Zhou et al. 2003 SZ63 W3110, ΔfocA-pflB::FRT ΔfrdZhou et al. 2003 ΔadhE::FRT ΔackA::FRT NC3 E. coli B/r, hsdR Dien et al.2001 KO11 pflB::Z. mobilis pdc adhB cat, Δfrd Ohta et al. 1991 LY52KO11, frdA::K. oxytoca casAB, lacY:: This example E. chrysanthemi celYSZ132 LY52, Δ(focA-pdc-adhB-pflB) ΔadhE::FRT This example ΔackA::FRT,ΔcasA SZ186 SZ132, ΔK. oxytoca casAB This example ΔE. chrysanthemi celY

Cultures were grown at 37° C. in modified Luria-Bertani (LB) broth (perliter: 10 g Difco tryptone, 5 g Difco yeast extract, 5 g sodiumchloride) or in NBS mineral salts medium supplemented with either 5% or10% sugar (glucose or sucrose). Antibiotics were included as needed forstrain constructions.

Standard methods were used for plasmid construction. Methods forchromosomal deletions, integration, and removable antibiotic resistancegenes have been previously described. Strains E. coli DH5α and S17-1were used as hosts for plasmid construction. Strain NC3 was used as anintermediate host to minimize problems associated with restrictionenzymes during P1 transduction from K-12 strains to B strains (Dien etal., 2001).

Seed cultures were prepared as described previously by Shukla et al.(2004) and Zhou et al., (2003) and used to inoculate small fermentationvessels (350 ml working volume, 35° C., 150 rpm agitation). Broth wasmaintained at pH 7.0 by the automatic addition of 6 N KOH. Plotted datarepresent an average of 2 or more replicates. Bars denoting the standarderror of the mean are included for averages of 3 or more fermentations.Maximum volumetric productivity for lactate was estimated from thesteepest region of each graph. No antibiotics were included during thegrowth of seed cultures or in fermentation broths.

Cell mass was estimated by measuring optical density at 550 nm (330 mgdry cell wt/l at 1.0 OD_(550nm)) Total organic acid production(primarily lactate) was measured by base (KOH) consumption. Acidicproducts were analyzed at the end of fermentation by high-performanceliquid chromatography. Ethanol was measured by gas chromatography.

Construction of Strain SZ132

Strain LY52 was constructed from KO11 by integrating the Klebsiellaoxytoca casAB genes (Moniruzzaman et al. 1997) for cellobioseutilization behind the stop codon of lacY and integrating the Erwiniachrysanthemi celY gene encoding endoglucanase (Zhou and Ingram, 1999)into the frdA gene. Previously characterized mutations in E. coli K-12(strain W3110) used to construct SZ63 (Zhou et al., 2003) for lactateproduction were sequentially transduced into LY52. Z. mobilis genes forethanol production were eliminated by P1 transduction of the ΔfocA-pflBdeletion from SZ31. The native E. coli alcohol dehydrogenase wasinactivated by P1 transduction of the adhE mutation from TC20. Acetatekinase (ackA) was deleted using the mutation in SZ61. Antibiotic genesused for selection were removed by FLP recombinase (Zhou et al., 2003).During the removal of antibiotic genes with FLP recombinase, an internalsegment of casAB was also deleted. Sequence analysis of casAB andpromoter revealed the presence of DNA regions very similar to therecognition site for FLP recombinase and are presumed to be responsiblefor this deletion.

The resulting strain was acclimated to minimal media by sequentiallysubculturing with a 1% inoculum. Both cell growth and lactate productionimproved during these transfers. Broth from the last transfer wasstreaked on solid medium for the isolation of clones. One was selectedand designated SZ132.

Construction of Strain SZ186

A further derivative of SZ132 was constructed in which all foreign geneswere removed. The K. oxytoca casAB and E. chrysanthemi celY genes weredeleted by homologous recombination using linear DNA. FLP recombinasewas used to eliminate antibiotic genes used during constructions. Theresulting strain, SZ186, contains only native E. coli genes.

Analysis of Lactic Acid Production

Analogous genetic mutations were constructed in derivatives of E. coliK-12 and E. coli B to produce SZ63 (Zhou et al., 2003) and SZ132,respectively. SZ132 was superior to SZ63 in terms of cell growth andlactate (D isomer) production (see FIG. 1A). In rich medium, SZ132completed the fermentation of 10% glucose in 48 h to produce over 1 molelactate/l of fermentation broth, twice that reported previously for E.coli K-12-based strains. Fermentations with SZ63 and 10% glucose stalledafter 72 h and produced only 840 mmoles lactate/l of broth after 120 h.In rich media, lactate yields were higher for SZ132 (95%) than for theK-12 strain SZ63 (88%). The maximum volumetric productivity for SZ132was 75 mmoles/1 h, 76% higher than for SZ63 (Table 2).

TABLE 2 Summary of Lactic Acid Fermentations Lactic Acid Produced E.coli Concentration Base adjusted Co-products produced (mM) strainsSubstrate (mM) concentration (mM) Yield (%) Succinate Acetate EthanolSZ132 NBS 10% Glu 556.01 ± 0.54 614.09 ± 0.54 91 32.11 ± 1.49 13.95 ±0.57 ≦1 SZ132 NBS 10% Glu + 792.23 ± 8.67 930.30 ± 8.67 86 78.92 ± 2.4511.56 ± 0.75 ≦1 Betaine SZ132 NBS 10% Suc  556.88 ± 33.21  609.78 ±33.21 92  2.79 ± 0.02 ≦1 ≦1 SZ132 NBS 10% Suc +  889.06 ± 157.53 1045.95 ± 157.53 88 38.00 ± 7.33 12.24 ± 3.72 ≦1 Betaine SZ186 NBS 10%Glu 600.41 ± 2.67 670.31 ± 2.94 99 ≦1 ≦1 ≦1 SZ186 NBS 10% Glu +  658.75± 21.37  744.39 ± 24.15 98 ≦1 ≦1 ≦1 Betaine SZ186 NBS 10% Suc  573.27 ±21.98  635.76 ± 24.38 95 ≦1 ≦1 ≦1 SZ186 NBS 10% Glu +  638.41 ± 33.59 718.06 ± 38.19 96 ≦1 ≦1 ≦1 Betaine SZ194 NBS 10% Glu +  717.60 + 51.51 823.85 + 65.48 96 ≦1 ≦1 ≦1 (Deposit Betaine No. NRRL B-30863) SZ194 LBpH 6.5 607.52 + 6.17 676.77 + 6.87 92 ≦1 ≦1 ≦1 10% Glu + Betaine SZ194LB pH 7.0 714.06 + 7.38 813.35 + 9.61 95 ≦1 ≦1 ≦1 10% Glu + BetaineSZ194 LB pH 7.5  913.16 + 25.73 1070.19 + 27.57 97 ≦1 ≦1 ≦1 10% Glu +Betaine SZ194 LB pH 8.0  903.22 + 21.51 1060.38 + 25.26 96 ≦1 ≦1 ≦1 10%Glu + Betaine SZ194 NBS pH 7.5 864.31 + 4.93 1019.89 + 5.81  95 ≦1 ≦1 ≦110% glu + betaine SZ194 NBS pH 7.5 1012.18 + 27.41 1227.60 + 31.16 95 ≦1≦1 ≦1 12% glu + betaine SZ194 NBS pH 7.5 1001.08 + 9.48  1217.02 + 13.5195 ≦1 ≦1 ≦1 14% glu + betaine SZ194 NBS pH 7.5 1003.65 + 12.74 1216.45 +16.48 93 ≦1 ≦1 ≦1 6 + 3 + 3% glu + betaine

In NBS mineral salts medium containing 5% glucose, cell yield andvolumetric productivity for SZ132 were twice that of SZ63 (see FIG. 1B).Strain SZ132 completed the fermentation of 5% glucose within 36 h, lessthan ¼ of the time required for SZ63. Under these conditions, cell yieldand volumetric productivity for fermentations with NBS mineral saltsmedium were only 25-35% of those with rich medium and 10% glucose.

Neither strain SZ132 nor SZ63 completed the fermentation of 10% glucosein NBS mineral salts medium within 144 h (see FIG. 1C). Lactate yieldsfor both strains were over 90% based on metabolized sugar. With NBSmineral salts medium containing 10% glucose, cell yield (0.83 g/l),lactate production (700 mmoles/l of fermentation broth), and volumetricproductivity (11.2 mmoles lactate/1 h) for SZ132 were approximatelytwo-fold higher than for SZ63. With NBS mineral salts medium and 10%glucose, volumetric productivity for SZ132 was less than 20% of thatobserved in rich medium.

Sucrose was fermented more slowly than glucose in rich medium and in NBSmineral salts medium. Previous studies have shown that SZ63 (pLOI3501)required 36 h to complete the fermentation of 5% sucrose in rich mediumbut was unable to complete the fermentation of 10% sucrose in thismedium. SZ132 completed the fermentation of 10% sucrose in rich mediumwithin 120 h and produced over 1 mole lactate/l of fermentation broth(see FIG. 1D), almost twice that previously reported for SZ63 harboringthe sucrose plasmid.

Volumetric productivity for SZ132 in NBS mineral salts medium containing10% sucrose (9.3 mmoles/1 h) was ⅓ of that observed in rich medium withsucrose, less than ⅛ that observed in rich medium containing 10% glucose(Table 2). Although 5% sucrose was fermented to completion in NBSmineral salts medium within 72 h (see FIG. 1E), 10% sucrose was notfully metabolized in this medium even with extended incubation times(FIG. 1F). Based on sugar metabolized, yields for sucrose ranged from86% to 93% in both media.

These results demonstrate that high levels of organic acids can beproduced from glucose and/or sucrose by modified strains of E. coli B.Maximum volumetric productivity was estimated at 75 mmoles lactate/1 hin rich medium (LB), over 3-fold higher than with NBS mineral saltsmedium. Many opportunities remain for improvement. Incubation timesrequired to complete the metabolism of 10% sucrose were 3-fold longerthan for 10% glucose in complex medium, longer still in mineral saltsmedium. Reducing fermentation times without the costly addition ofcomplex nutrients may be essential. Identifying the constituents thatincrease growth and productivity could substantially reduce costsassociated with fermentation and also offer an opportunity to reduceexpenses associated with lactate purification and waste treatment.

FIGS. 2-5 illustrate progress of lactic acid (D isomer) production byvarious embodiments, namely SZ132, SZ186, and SZ194 (Deposit No. NRRLB-30863) of the invention under various fermentation conditions in NBSmineral salts medium.

Example 2 Preparation of E. Coli Strain SZ194

Strains and plasmids used in the preparation of Strain SZ194 are listedin Table 3. Cultures were grown at 37° C. in modified Luria broth (perliter: 10 g Difco tryptone, 5 g Difco yeast extract, 5 g sodiumchloride) (Miller, J. H. 1992 A Short Course in Bacterial Genetics: ALaboratory Manual and Handbook for Escherichia coli and RelatedBacteria. Cold Spring Harbor Press, Cold Spring Harbor, N.Y.) or in NBSmineral salts medium (Causey, T. B. et al. 2004, “EngineeringEscherichia coli for efficient conversion of glucose to pyruvate,” Proc.Natl. Acad. Sci. USA 101:2235-2240) supplemented with 1 mM betaine and2%-14% (w/v) sugar (glucose or sucrose). When needed, ampicillin (50mg/L) and kanamycin (50 mg/L) were used for strain constructions.

TABLE 3 E. coli Strains and Plasmids Relevant Characteristics SourcesStrains SZ132 Δ(focA-Z. mobilis pdc-adhB-pflB) Zhou et al. adhE::FRTΔack::FRTΔfrd, frdA:: (2005) E. chrysanthemi celY lacY::K. oxytoca casABSZ136 SZ132, selected for rapid growth and This example fermentation in10% sucrose SZ162 SZ136, Δ frdBC::FRT Δ adhE::FRT This example SZ186SZ162, Δ casAB::FRT Δ celY::FRT This example SZ186 SZ186, selected forrapid growth and This example fermentation in 10% glucose Plasmids pKD46Bla γ β exo (Red recombinase), Datsenko and temperature conditionalpSC101 replicon Wanner (2000) pFT-A Bla flp temperature conditionalPosfai et al. pSC101 replicon (1997) pLOI2511 colE1, FRT-kan-FRT, blapLOI3924 colE1, bla kan lacY′-FRT-Kan-FRT-lacYA

Standard methods were used for DNA amplification, enzyme digestion,purification and plasmid construction (Miller et al., 1992; Sambrook andRussell, 2001). Methods for chromosomal gene deletion and integrationhave been previously described (Causey et al., 2004; Datsenko andWanner, 2000; Martinez-Morales et al., 1999; Zhou et al., 2003a).

Plasmid pLOI3924 was constructed to facilitate deletion of the casABgenes by cloning lacY and lacA genes using ORFmers (Sigma-Genosis, TheWoodlands, Tex.), and inserting the FRT-kan-FRT cassette (SmaIdigestion) from pLOI2511 between the NdeI site in the carboxyterminus oflacY and the N-terminal ATG of lacA. The amplified fragment (forwardORFmer for lacY; reverse ORFmer for lacA) from this plasmid was used forchromosomal integration, deleting the casAB genes. Hybrid primers usedfor additional gene deletions and contained sequence corresponding toapproximately 45 base pairs of the beginning or end of the target geneplus 20 base pair of DNA sequence corresponding to the FRT-flankedkanamycin cassette are described in Table 4.

TABLE 4 Primers SEQ ID Primer NO: Sequence sense primer for 1ATGGCTGAGATGAAAAACCTGAAAAT frdBC deletion TGAGGTGGTGCGCTATAACGTGTAGGCTGGAGCTGCTTC antisense primer 2 TTACCAGTACAGGGCAACAAACAGGA for frdBCdeletion TTACGATGGTGGCAACCACCATATGAA TATCCTCCTTAG sense primer for 3ATGGCTGTTACTAATGTCGCTGAACTT adhE deletion AACGCACTCGTAGAGCGTGTGTAGGCTGGAGCTGCTTC antisense primer 4 TTAAGCGGATTTTTTCGCTTTTTTCTCA for adhEdeletion GCTTTAGCCGGAGCAGCCATATGAATA TCCTCCTTAG sense primer for 5GATAAGGCGGAAGCAGCCAATAAGAA celY deletion GGAGAAGGCGAATGGCTGAGTGTAGGCTGGAGCTGCTTC antisense primer 6 CCAGAATACCGGTTCGTCAGAACGCTT for celYdeletion TGGATTTGGATTAATCATCATATGAAT ATCCTCCTTAG

Unless otherwise specified, NBS mineral salts medium (Causey et al.,2004) containing 1 mM betaine and 10% sugar (glucose or sucrose) wasused in all fermentations (pH 7.0). Seed cultures were prepared asdescribed previously (Zhou et al., 2003) and used to inoculate 500 mlfermentation vessels (350 ml working volume, 35° C., 150 rpm agitation)to an initial density of 33 mg cdw l⁻¹. Where indicated, betaine (1 mM)was also added. Broth pH was maintained by automatic addition of 6 NKOH. A total of 12% (w/v) glucose was used in the fed batchfermentations (6%+3%+3%) as follows: 308 ml of NBS medium containing 21grams of glucose. After 24 h and 48 h, 21 ml of 50% glucose was slowlyadded into each vessel.

Cells from pH-controlled fermentations were serially transferred atvarious times (24 or 48 h) to facilitate metabolic evolution throughgrowth-based selection. Sequentially transferred cultures wereinoculated at an initial density of 33 mg cdw l⁻¹. Clones isolated atthe end of selections were assigned new strain designations.

Cell mass was estimated by measuring optical density at 550 nm using aBausch & Lomb Spectronic 70 spectrophotometer. Total organic acidproduction (primarily lactate) was estimated by base (KOH) consumptionfor pH maintenance. Acidic products and chiral purity were analyzed atthe end of fermentation by high-performance liquid chromatography (Zhouet al., 2003a). Plotted data represent an average of 2 or morereplicates. Bars denoting the standard deviation are included foraverages of 3 or more fermentations.

Analysis of Lactic Acid Production

Betaine, a protective osmolyte, was highly beneficial for cell growthand lactate production by SZ132 in mineral salts medium containing highsugar concentrations, presumably due to insufficient carbon partitioninginto the biosynthesis of native osmolytes such as glutamate andtrehalose (Purvis et al., 2005). Serial transfers of SZ132 were carriedout in mineral salts medium containing 10% sucrose to select for strainswith equivalent performance in the absence of betaine (FIGS. 6A and 6B).Energy production for growth in strain SZ132 is dependent on glycolyticflux with lactate as the dominant route for NADH oxidation, providing agrowth-basis selection. Growth and acid production (base consumption)improved steadily during serial transfers. In the final transfers, 10%sucrose was fermented to completion without added betaine. A clone wasisolated from this culture and designated strain SZ136. This strainproduced twice the cell yield of the parent, SZ132, and 3-fold highertiters of lactate after 96 h (FIG. 6). However, SZ136 also producedhigher levels of succinate and ethanol than SZ132 (Table 5), reducinglactate yield (based on metabolized sugar).

TABLE 5 Products from glucose fermentations Lactate Co-products (mmoll⁻¹) Strain Conditions^(a) mmol l⁻¹ Yield (%)^(b) Succinate AcetateEthanol SZ132 NBS + 930 ± 9 86 79 ± 2 12 ± 1 <1 betaine SZ136 NBS 739 67126 8 115 SZ162 NBS  660 ± 27 96 <1 <1 <1 SZ186 NBS 670 ± 3 99 <1 <1 <1SZ186 NBS +  744 ± 24 98 <1 <1 <1 betaine SZ194 NBS +  824 + 65 96 <1 <1<1 betaine SZ194 Luria broth 677 ± 7 92 <1 <1 <1 pH 6.5 SZ194 Luriabroth  813 ± 10 95 <1 <1 <1 pH 7.0 SZ194 Luria broth 1070 ± 28 97 <1 <1<1 pH 7.5 SZ194 Luria broth 1060 ± 25 96 <1 <1 <1 pH 8.0 SZ194 NBS, pH7.5 + 1020 ± 6  95 <1 <1 <1 betaine SZ194 NBS pH 7.5 1228 ± 31 95 <1 <1<1 12% glucose + betaine SZ194 NBS, pH 7.5 1217 ± 14 95 <1 <1 <1 14%glucose + betaine SZ194 NBS, pH 7.5 1216 ± 17 93 <1 <1 <1 glucose (6 +3 + 3%) + betaine ^(a)NBS mineral salts medium containing 10% glucose(pH 7.0) unless specified otherwise. Where indicated, 1 mM betaine wasalso added. ^(b)Yields are based on metabolized sugar assuming a maximumtheoretical yield of 2 moles of lactate per mole of hexose (equal weightconversion).

Improvements in growth in SZ132 on 10% (w/v) sucrose appear to have beenaccompanied by mutations that improved growth but also partiallyrestored the function of mutated genes for co-product pathways. Thefumarate reductase mutation in strain SZ132 is poorly characterized andwas originally obtained as a Tn5 deletion (Ohta et al., 1991), followedby insertion of celY between frdA and frdB (Zhou et al., 2005). Thealcohol dehydrogenase gene was disrupted by insertion of an antibioticmarker with flanking FRT sites. Flippase was then used to remove theantibiotic gene leaving only an FRT region. Further deletion of codingregions for frdBC and adhE to produce SZ162 eliminated both co-productsbut also reduced growth and the final lactate titer due to incompletesugar utilization (Table 5). Additional deletions were also made in thisstrain to eliminate foreign genes that had been previously integratedfor cellulose utilization (Zhou et al., 2005): casAB (cellobiosetransporter gene) from Klebsiella oxytoca and celY (endoglucanase) fromErwinia chrysanthemi. The resulting strain, SZ186, produced negligiblelevels of co-products but failed to completely utilize 10% sugar inmineral salts medium with or without betaine (FIG. 7A; Table 5).However, yields based on metabolized sugar were high (96%-99%) for bothSZ162 and SZ186.

Deletions in SZ136 that eliminated co-product pathways (SZ186) alsoreduced cell yield by almost half, adversely affecting the partitioningof carbon into biosynthesis. Metabolic evolution was used to co-select aderivative of SZ186 with both improved growth and fermentationperformance in the presence of 1 mM betaine and 10% glucose (FIGS. 7Aand 7B). Cell yield and organic acid production increased concurrentlyduring the initial rounds of selection. A single clone was isolated fromthe last enrichment and designated SZ194.

Strain SZ194 grew more rapidly than SZ186 and reached a higher cellyield. Lactate concentrations of up to 900 mM were produced by SZ194 insome fermentations, consistently higher than those of SZ186 (Table 5).Both strains produced lactate from glucose at near theoretical yieldswith minimal co-products. With both strains, however, sugar remainedunused at pH 7.0 even after prolonged incubation. At pH 7.0, the 800-900mM lactate produced from 10% (w/v) glucose is well above the maximumlactate concentration needed to inhibit growth at pH 7.0 and may alsoinhibit further glucose metabolism.

Two factors were explored as possible causes for the incompletefermentation of 10% (w/v) sugar by SZ194: an unknown nutritional defectand lactate tolerance. Replacing mineral salts medium containing 1 mMbetaine with Luria broth (rich medium) at pH 7.0 had little effect onlactate yield (Table 5) or lactate production (Table 6). Lactatetoxicity was tested by comparing the effect of pH on fermentation (Table5). The toxicity of weak organic acids such as lactate is related inpart to the uncoupling action of the conjugate neutral form (Warnecke etal., 2005), which in turn is inversely related to pH. A similar trendwas observed for fermentation. In Luria broth, final lactate titers werelowest at pH 6.5 and highest at pH 7.5 and pH 8.0. Changes in pH hadless effect on cell yield. At pH 7.5, 10% (w/v) glucose was fermented tocompletion in 72 h using Luria broth.

TABLE 6 Comparison of lactate productivity Lactate Cell Volumetric^(b)Specific^(b) Volumetric^(b) Fermentation titer yield productivityproductivity productivity Strain conditions^(a) (mmol l⁻¹) (g l⁻¹) (mmoll⁻¹h⁻¹) (mmol g⁻¹h⁻¹) (g l⁻¹h⁻¹) SZ132 pH 7.0 930 2.07 24.6 11.9 2.21SZ194 pH 7.0 824 1.73 18.5 10.7 1.67 SZ194 pH 7.5 1020 1.67 23.8 14.22.14 SZ194 Luria broth, pH 1070 1.75 24.7 14.1 2.22 7.5 no betaine added^(a)Mineral salts (NBS) containing 10% (w/v) glucose and1 mM betaineunless otherwise specified. ^(b)Averaged values for the most productive24-h period.

The benefit of this increase in pH was confirmed in mineral salts mediumcontaining 1 mM betaine (FIG. 8; Table 5). At pH 7.5, 10% and 12% (w/v)glucose were fermented to completion, producing over 1 mol lactate l⁻¹with only trace amounts of co-products (FIG. 3A). Product yields of 0.95g lactate per g glucose represent 95% of the maximum theoretical yieldbased on total sugar added to the fermentation. Addition of higherlevels of sugar did not further increase final lactate titers. Similarfinal titers were observed during fed-batch experiments (FIG. 8B) anddid not increase further when additional sugar was added. Final lactatetiters of approximately 1.0-1.2 M appear to represent an upper limit forsugar metabolism at pH 7.5 by SZ194 (Table 5).

It is interesting to note that pH 7.5, the optimal pH for fermentation,is very close to that reported for the cytoplasm of E. coli (Axe et al.,1995; Warnecke et al., 2005). Although no lactate transporter genes havebeen identified in E. coli, several studies have provided evidence fortheir presence in E. coli and lactic acid bacteria (Axe et al., 1995;Konings, 2002; Poolman, 2002). These transporters are presumed to belactate/H⁺ symporters, activities that may increase in efficiency withincreases in external pH. According to the “energy recycling model”(Michels et al., 1979), carrier-mediated efflux of metabolic endproducts such as lactate can lead to generation of an electrochemicalproton gradient across the membrane and contribute to ATP production.Lactate efflux in lactic acid bacteria has been estimated to contribute30% of total cellular energy (van Maris et al., 2004a). Since E. coliSZ194 and lactic acid bacteria metabolize glucose by similar pathways,it is possible that additional ATP is also produced by lactate efflux inE. coli.

The chiral purity of lactate produced by SZ194 was examined and found tobe greater than 95% D-lactate. Although good, this chiral purity islower than that of the parent strain, SZ132 (99.5% D-lactate) (Zhou etal., 2005). The source of this chiral impurity is unknown.

According to the subject invention, lactate titers of over 1 M can beproduced by E. coli SZ194 at pH 7.5 in mineral salts medium supplementedwith 1 mM betaine. In this medium, lactate productivity and cell yieldfor SZ194 were equivalent to that in Luria broth (Table 6). The finallactate titer of 110 g l⁻¹ and yield (0.95 g lactate g glucose⁻¹) forstrain SZ194 compare favorably with lactic acid bacteria such as L.helveticus (Kyla-Nikkila et al., 2000) and L. delbrueckii (Demirci etal., 1992) and exceed the performance of previously engineeredbiocatalysts in rich medium or in mineral salts (Dien et al., 2001;Porro et al., 1999; Saitoh et al. 2005; van Maris et al., 2004b).

Example 3 Materials and Methods Strains, Plasmids, Media and GrowthConditions

E. coli strains, plasmids and primers utilized in this study are listedin Table 7. Strain SZ194 was previously constructed from a derivative ofE. coli B (ATCC 11303) and served as a starting point for constructions(see Example 2 and Zhou et al., 2006). During strain constructions,cultures were grown aerobically at 30° C., 37° C., or 39° C. in Luriabroth (per liter: 10 g Difco tryptone, 5 g Difco yeast extract and 5 gsodium chloride) (Miller 1992) containing 2% (w/v) glucose or arabinose.Ampicillin (50 mg/L), tetracycline (12.5 or 6.25 mg/L), or kanamycin (25or 50 mg/L) were added as needed. For fermentation tests, strains weregrown without antibiotics at 37° C. in NBS mineral salts medium (Causeyet al., 2004) supplemented with 1 mM betaine and 2-12% (w/v) glucose.MOPS buffer (100 mM, pH 7.4) was added to solid and liquid medium underconditions which lacked pH control (plates, tubes, shaken flasks).

Genetic Methods

Manufacturer protocols and standard methods (Miller 1992, Sambrook andRussell 2001) were followed for DNA purification (Qiagen), restrictionendonuclease digestion (New England Biolabs), DNA amplification(Stratagene and Invitrogen) and transformation. Methods for chromosomaldeletions and integration have been described previously (Causey et al.,2004, Zhou et. al, 2003, Datsenko and Wanner 2000, Martinez-Morales etal., 1999). Hybrid primers (Table 7) containing sequence homologous tothe 50 nucleotides of the beginning or end of the mgsA gene (italics)plus 20 nucleotides corresponding to the sequence of the FRT-flankedkanamycin cassette (underlined) of pKD4 were used for deletion of thenative mgsA gene. Plasmid pLOI2398 was constructed previously tofacilitate integration of Pedioccoccus acidilactici ldhL into thechromosomal ldhA gene of E. coli (Zhou et al., 2003a).

Fermentations

Pre-inoculum was grown by inoculating a colony into a 250-ml flask (100ml NBS medium with 2% (w/v) glucose and 100 mM MOPS, pH 7.4). After 16 h(37° C., 120 rpm), this pre-inoculum was diluted into 500-mlfermentation vessels containing 350 ml NBS media (5-12% sugar, with orwithout 1 mM betaine) to provide 33 mg dcw l⁻¹. After 24-h (37° C., 150rpm, pH controlled at 7.0), this culture was used to provide a startinginoculum of 33 mg dcw l⁻¹. Volumetric productivity is reported for themost active 24-h period. Specific productivity was calculated as thequotient of volumetric productivity divided by cell mass at 24 h.

Metabolic Evolution

Cells from pH-controlled fermentations were serially transferred at 24or 48 h intervals to facilitate metabolic evolution though competitive,growth-based selection. At each transfer, inocula were diluted (1/100 to1/350) into pre-warmed, fresh media. Clones isolated from theseselections were assigned new strain designations.

Analyses

Cell mass was estimated by measuring the optical density at 550 nm usinga Bausch & Lomb Spectronic 70 spectrophotometer. Total organic acidproduction, primarily lactate, was estimated by KOH consumption used tomaintain pH 7.0. Acidic products and chiral purity were analyzed at theend of fermentation by high-performance liquid chromatography. Estimatesof organic acid by base consumption were consistently lower thanmeasurements of lactate by HPLC, presumably due to mineral metabolism.

Results and Discussion Restoring Chiral Purity for D-(−)-LactateProduction

Strain SZ194 has been shown to efficiently produce D-(−)-lactate fromglucose at 99% chiral purity in mineral salts medium (Zhou et al.,2006). Betaine increased lactate productivity (titer and rate) with highconcentrations of sugar but also decreased chiral purity to 95% (Table8). There are several possible sources of L-(+)-lactate in E. coli (FIG.9A). L-(+)-lactate can be produced from lactaldehyde, an intermediate inthe catabolism of rhamose or fucose (Badia et al., 1991), both absent inour media, and as a product from the Methylglyoxal Bypass of glycolysis(FIGS. 9A and 9B). The Methlyglyoxal Bypass represents a short spilloverpathway that is induced by accumulation of dihydroxyacetone-phosphateduring rapid glycolysis, and by a phosphate limitation for ATPsynthesis. Both the accumulation of dihydroxyacetone-phosphate andphosphate limitation could be exacerbated by high rates of glycolyticflux. To test this hypothesis, the mgsA gene encoding the firstcommitted step, methylglyoxal synthase, was deleted. The resultingstrain, TG112, produced chirally pure D-(−)-lactate (Tables 8 and 9;FIGS. 10A and 10B). Growth and initial productivity were increased bythis deletion in comparison to SZ194. Yields based on HPLC analyses weresimilar (Table 8).

Further improvements in TG112 were selected by metabolic evolutionduring 81 days of growth (FIG. 11). Fermenting cultures were seriallytransferred in mineral salts medium containing 10% (w/v) glucose, 12%(w/v) glucose, and 12% (w/v) glucose with 1 mM betaine. One clone wasisolated at day 28 (TG113) and another at the end of enrichment (TG114).D-(−)-lactate productivity (rate, titer, and yield) and cell yieldimproved during this process (FIGS. 10A and 10B; Table 8 and Table 9).Fermentation with SZ114 was substantially complete within 48 h in mostexperiments, with a final yield of 0.98 g D-(−)-lactate g⁻¹ glucose.High inocula provided a modest further improvement in specific andvolumetric productivities. Co-products and chiral impurities were belowdetection (<0.1%) with these mgsA-deleted strains. Production ofD-(−)-lactate by TG114 compares favorably with other biocatalysts andoffers high productivity, titer, yield and chiral purity with simplemedia and fermentation conditions (Table 10).

Production of Chirally Pure L-(+)-lactate

The D-(−)-lactate strain, SZ194, was re-engineered to produce primarilyL-(+)-lactate by replacing the native ldhA gene encoding a D-(−)-lactatedehydrogenase with the ldhL gene from P. acidilactici encodingL-(+)-lactate dehydrogenase (Zhou et al., 2003a). The resulting strain,TG102 produced primarily L-(+)-lactate and was serially transferred inminimal medium containing 5% (w/v) glucose, 10% (w/v) glucose and 10%(w/v) glucose containing 1 mM betaine to select for improved growth andproductivity. After 24 days, one clone was selected and designatedTG103. Although lactate productivity improved due to an increase inglycolytic flux (FIGS. 10C and 10D; Table 9), L-(+)-lactate wascontaminated with 5% D-(−)-lactate (Table 8). Since the MethylglyoxalBypass has the potential to produce both chiral forms of lactate, mgsAwas identified as the most likely source of chiral impurity. Absolutechiral purity was restored after deletion of mgsA. The resulting strain,TG105, produced only L-(+)-lactate (FIGS. 10 and 10D; Table 8). Furtherimprovements were by co-selecting growth and productivity during serialtransfers in mineral salts medium containing 10%-12% (w/v) glucose and 1mM betaine (inoculum dilution of 1:100 to 1:350). TG106 and TG107 wereisolated as intermediate strains after 10 and 22 transfers, respectively(FIGS. 10E and 10F). Strain TG108 was isolated after 99 days. Allproduced only L-(+)-lactate at high yields with minimum levels ofco-products (Table 8). Volumetric productivities in 12% (w/v) glucoseand cell yield increased during strain selection although specificproductivity remained essentially constant (Table 9). Small increases inmaximum volumetric productivity (most active 24-h period) were observedwith higher inocula.

Strain TG108 was compared to other biocatalysts for L-(+)-lactateproduction (Table 10). The titer and yield for this strain were higherthan those reported for other organisms. Other advantages include simplefermentation conditions and medium, and chiral purity.

Conclusions

High titers (>100 gl⁻¹ in 48 h) of chirally pure L-(+) and D-(−)-lactate(>99.9% chiral purity) can be readily produced by recombinant E. coli Bin mineral salts medium supplemented with 1 mM betaine. Elimination ofthe Methylglyxal Bypass was essential to eliminate impurities in boththe D-(+) and L-(−) enantiomers of lactate.

Example 4 Construction of TG128 by Removal of all Foreign DNA from TG114

To facilitate commercial application of recombinant E. coli strains forlactate production, a further derivative of TG114 was constructed inwhich all extraneous DNA that had been left behind in the chromosomeduring previous genetic engineering was removed. DNA removed includedscar regions containing the FRT recognition site for the flippase(recombinase) used to remove antibiotic markers, small fragments of DNAfrom Zymomonas mobilis, part of Klebsiella oxytoca casAB, and part ofErwinia chrysanthemi celY. These foreign DNA segments were completelyeliminated leaving only native chromosomal DNA in which central regionsof selected genes have been deleted to improve the production oflactate.

Strains, Plasmids, Media and Growth Conditions

E. coli strains, plasmids and primers used in this study a listed inTable 11. Strain TG114 was formerly constructed from a derivative of E.coli B (ATCC 11303) and served as a starting point for constructions(Grabar et al., 2006). During strain constructions, cultures were grownaerobically at 30° C., 37° C., or 39° C. in Luria broth (per liter: 10 gDifco tryptone, 5 g Difco yeast extract and 5 g sodium chloride) (Miller1992) containing 2% (w/v) glucose or arabinose or 10% sucrose.Ampicillin (50 mg/L), chlorotetracycline (10 mg/L), or chloramphenicol(40 mg/L) were added as needed.

Cultures were maintained on plates containing NBS mineral salts medium(Causey et al., 2004) supplemented with 2% (w/v) glucose. MOPS buffer(100 mM, pH 7.4) was added to solid and liquid medium under conditionswhich lacked pH control (plates, tubes, shaken flasks). For fermentationtests, strains were grown without antibiotics at 37° C. in AM1 mineralsalts medium (per liter: 2.63 g (NH₄)₂HPO₄, 0.87 g NH₄H₂PO₄, 0.37 gMgSO₄.7H₂O, 2.4 mg FeCl₃, 0.3 mg CoCl₂.6H₂O, 0.15 mg CuCl₂, 0.3 mgZnCl₂.4H₂O, 0.3 mg NaMoO₄, 0.075 mg H₃BO₃, 0.075 mg MnCl₂.4H₂O₂, 1 mMbetaine and 120 g/L glucose).

Genetic Methods

Manufacturer protocols and standard methods (Miller 1992, Sambrook andRussell 2001) were followed for cloning of genes (Invitrogen), DNApurification (Qiagen), restriction endonuclease digestion (New EnglandBiolabs), DNA amplification (Stratagene and Invitrogen) andtransformation. Methods for chromosomal deletions and integration havebeen described previously (Causey et al., 2004, Zhou et. al, 2003,Datsenko and Wanner 2000, Martinez-Morales et al., 1999). A descriptionof the plasmids and the primers used are listed in Table 11.

Plasmid Constructions

Plasmid pLOI4411 was generated by designing primers that amplifiedwithin the frdABCD operon of E. coli B gDNA, ‘frdA frdB frdC and frdD’,and subsequent ligation into the Invitrogen cloning vector, pCR2.1-TOPO(Table 11). Plasmids pLOI4412, pLOI4413, pLOI4415 and pLOI4416 wereconstructed in a similar approach in order to clone the native genes ofinterest, ackA, adhE, focA-plfB and mgsA, respectively.

Plasmids encoding the seamless gene knockouts were generated usingantisense primers. Antisense primers with 5′ phosphate groups weredesigned to amplify the entire plasmid minus the gene region to beomitted (FIG. 12). For example, pLOI4417 was generated by performing PCRon pLOI4411 with a primer that annealed to the 3′ end of frdA, extendingupstream, and a primer that annealed within frdC, extending downstream.The resulting 4263 by PCR product was treated with restriction enzymeDpnI to digest the native pLOI4411 plasmid. Digested PCR products weresubsequently self-ligated in order to generate the new plasmid,pLOI4417. Plasmids pLOI4418. pLOI4419, pLOI4421 and pLOI4422 weregenerated in a similar fashion using primer sets listed in Table 11.These plasmids served as a PCR template to amplify linear DNA thatcontained the desired deletion and was devoid of all heterologoussequence. This linear DNA was used to replace FRT scar regions,heterologous DNA, and sacB by homologous recombination (doublecross-over event). In this way, seamless deletions of selected geneswere made on the chromosome.

Removal of FRT Scar and Heterologous DNA from TG114

The ˜85 by FLP recognition target (FRT) scars left behind by theone-step deletion method of Datsenko and Wanner (2000) were removed by atwo-step approach. First, the FRT sites were individually targeted by acircular FRT-cat-sacB cassette resulting in a single cross-overintegration of this cassette into an FRT scar on the chromosome(FRT-cat-sacB-FRT). Circular DNA containing the cat-sacB-FRT cassettewas constructed as follows: 1. PCR amplification of the FRT-cat-sacBcassette using plasmid pLOI4151 as the template. The amplified cassetteincluded flanking PstI sites; 2) Digestion with PstI followed byself-ligation to produce closed circles incapable of autonomousreplication. This circular DNA was used for integration. Expression ofthe cat gene conferred chloramphenicol resistance and allowed directselection of cells containing the integration.

In the second step, the sacB gene allowed a direct selection of cells inwhich the DNA region containing sacB has been removed by homologousrecombination (double cross-over event). Cells expressing sacB in thepresence of 10% sucrose (Ausubel et al., 2005; Lee et al., 2001) werekilled and lysed by the intracellular production of polysaccharide. Withthis method, recombinants in which DNA had been inserted to replace sacBcould be selected from large populations. In this example, integrationof a linear DNA fragment via a double-crossover event resulted in aclean knockout strain containing only native DNA or native DNA withdeletions, lacking all heterologous DNA. Native DNA sequence or nativesequence containing a desired gene deletion was used in this second stepto completely remove FRT scar regions and all heterologous DNA fromstrain TG114.

Following electroporation with the linear DNA fragment, the cells wereincubated with shaking at 37° C. for 4 hours in 1 mL SOC medium. Afterthe 4 hour outgrown, the cells were incubated for 16-20 hours in 50 mLLB with no salt (per liter: 10 g Difco tryptone, 5 g Difco yeastextract) supplemented with 10% (w/v) sucrose. Then the cells were struckonto salt-less LB agar plates supplemented with 5% sucrose. The majorityof cells retaining the FRT-cat-sacB were not viable after prolongedperiods in the presence of sucrose. Viable cells forming colonies weredevoid of sacB, and scar regions.

This method was used sequentially to eliminate all 5 FRT scars presentin TG114 and to restore the lac operon. Primers, plasmids, and strainsused in this process are summarized in Table 11. The casAB genesintegrated into lacA were also removed and replaced with wild typesequence in this region using a modification of this two-step method.Fragments of Erwinia chrysanthemi celY (and Z. mobilis DNA) integratedinto frdA were removed during the construction of the seamless frdBCdeletion. The resulting strain, TG128, is devoid of FRT scars andcontains only native DNA sequence with deleted regions in the genesindicated in Table 11. A comparison of the original sequence in theregion of gene deletions is shown for TG114 and TG128 (Table 12).

Restoration of Native lac Operon

TG114 contained segments of heterologous DNA (DNA fragments fromZymononas mobilis, Klebsiella oxytoca casAB, and part of Erwiniachrysanthemi celY) from prior constructions in the lacy, lacA region(Grabar et al., 2006). These were removed from TG120 to produce TG122and are absent in subsequent derivatives of TG122. Primers for thisconstruction are listed in Table 11. To accomplish this, the nativelacZ′ to cynX region was amplified from E. coli B and cloned intopCR2.1-TOPO to produce pLOI3956. To facilitate selection ofrecombinants, the central region of pLOI3956 (lacZ′-lacA′) was replacedwith a cassette containing cat and sacB genes as follows. With pLOI3956as a template, antisense primers containing an NheI sites were used toamplify lacZ′, pCR2.1, and cynX (omitting part of lacZ, lacy, lacA andpart of cynX′). A second set of primers containing NheI sites was usedto amplify a cat-sacB cassette from plasmid pEL04 (originally known aspK04, Ausubel et al., 2005 and Lee et al., 2001). After digestion withNheI, these PCR products were ligated to produce pLOI3957, a derivativeof pCR2.1 that contains lacZ′-sacB-cat-cynX′. Using plasmid pLOI3957 asa template, the lacZ′-sacB-cat-cynX′ region was amplified by PCR andintegrated into TG120 with selection for chloramphenicol resistance toproduce TG121. Using pLOI3956 as a template, the wild typelacZ′-lacY-lacA-cynX′ region was amplified by PCR and integrated intoTG121. Integrants containing the native sequence of the lacZYA operonwere selected by the absence of sacB function during growth in thepresence of sucrose. One of these was designated TG122. Strain TG122 wasan intermediate strain during the construction of TG128.

Fermentations

Pre-inoculum was grown by inoculating a colony into a 250-ml flaskcontaining 100 ml of NBS medium (Causey et al., 2004) with 2% (w/v)glucose and 100 mM MOPS (pH 7.4). After 16 h (37° C., 120 rpm), thispre-inoculum was diluted into 500-ml fermentation vessels containing 350ml AF1 mineral salts media (12% sugar) to provide 33 mg dcw/L. After24-h (37° C., 150 rpm, pH controlled at 7.0), the resulting culture wasused to provide a starting inoculum of 33 mg dcw/L and incubated underthe same conditions for 96 h. Samples were removed for analyses.

Analyses

Cell mass was estimated by measuring the optical density at 550 nm usinga Bausch & Lomb Spectronic 70 spectrophotometer. Total organic acidproduction, primarily lactate, was estimated by KOH consumption used tomaintain pH 7.0. Acidic products and chiral purity were analyzed at theend of fermentation by high-performance liquid chromatography. Estimatesof organic acid by base consumption were consistently lower thanmeasurements of lactate by HPLC, presumably due to mineral metabolism.

Fermentation of Glucose by TG128

Strain TG114 was subjected to intensive genetic manipulation to removeFRT scars and other extraneous DNA. The resulting organism, strainTG128, contains only native, wild-type DNA sequence and seamlessdeletions of genes to eliminate unwanted fermentation products.Fermentation performance of this strain was essentially equivalent tothat for TG114, lactate yields of 96-98% of the maximum theoreticalyield (Table 13).

Selection of Thermotolerant Mutants for Lactate Production by MetabolicEvolution

Metabolic evolution was used to select strains capable of efficientlactate production at elevated temperatures. Cells from pH-controlledfermentations were serially transferred at 24 h intervals to facilitatemetabolic evolution though competitive, growth-based selection. At eachtransfer, inocula were diluted (1/100 to 1/350) into pre-warmed, freshmedia. Incubation temperature was increased by a fraction of a degree asgrowth permitted to facilitate the isolation of thermotolerant strains.Strain TG128 ferments optimally at 37° C. Mutants were obtained byincrementally increasing the incubation temperature during successivetransfers. With this approach, new strains were selected from TG128 thatare now capable of efficient fermentation at 39° C. (strain TG129) and43° C. (strain TG130). Yields for both thermotolerant strains atelevated temperature were equivalent to TG114 at 37° C. (Table 13).

Fermentation of Glucose by TG128

Strain TG114 was subjected to intensive genetic manipulation to removeFRT scars and other extraneous DNA. The resulting organism, strainTG128, contains only native, wild-type DNA sequence and seamlessdeletions of genes to eliminate unwanted fermentation products.Fermentation performance of this strain was essentially equivalent tothat for TG114, lactate yields of 96-98% of the maximum theoreticalyield (Table 13).

Selection of Thermotolerant Mutants for Lactate Production

Metabolic evolution was used to select strains capable of efficientlactate production at elevated temperatures. Serial transfers intofermentors in which temperature was increased by a fraction of a degreeallowed the isolation of TG129 which ferments optimally at 39° C. andTG130 which ferments optimally at 43° C. Yields for both at elevatedtemperature were equivalent to TG114 at 37° C. (Table 13).

TABLE 7 E. coli strains, plasmids and primers used in this study Plasmidor Strain Relevant Characteristics Sources Strains SZ194 pflB frd adhEackA Zhou et al. (2006) TG102 SZ194, ΔldhA::ldhL-FRT This study TG103Mutant of TG102 with improved growth and This study ldhL activity TG105TG103, ΔmgsA::FRT This study TG106, TG107 Mutants of TG105 with improvedgrowth and This study and TG108 ldhL activity TG112 SZ194, ΔmgsA::FRTThis study TG113 and Mutants of TG112 with improved growth and Thisstudy TG114 ldhA activity Plasmids pKD46 bla γ β exo (Red recombinase),temperature Datsenko and conditional pSC101 replicon Wanner (2000) pFT-Abla flp temperature conditional pSC101 Posfai et al. (1997) repliconpKD4 bla kan; R6K ori; FRT-kan-FRT cassette Datsenko and Wanner (2000)PLO12398 kan; ldhA′-ldhL-FRT-tet-FRT-′ldhA; R6K ori Zhou et al. (2003)Primers Sense primer for Atgtacattatggaactgacgactcgcactttacctgcgcgg Thisstudy mgsA deletion aaacatat gtgtaggctggagctgcttc (SEQ ID NO: 7)Antisense primer Ttacttcagacggtccgcgagataacgctgataatcgggga This studyfor mgsA deletion tcagaatat catatgaatatcctccttag (SEQ ID NO: 8)

TABLE 8 Products from glucose fermentations Lactate Yield ChiralCo-products (mmol l⁻¹) Strain Conditions^(a) mmol l⁻¹ (%)^(b) Purity (%)Succinate Acetate Ethanol SZ194 NBS, pH 7.5 + 1228 ± 31 95 95 <1 <1 <1betaine TG102 NBS 555 ± 6 99 99.5 <1 <1 <1 5% glucose TG102 NBS  697 ±13 96 99.5 <1 <1 <1 10% glucose TG102 NBS 1025 ± 18 94 95 <1 <1 <1 10%glucose + betaine TG103 NBS 1080 ± 15 95 95 <1 <1 <1 10% glucose +betaine TG105 NBS +  969 ± 20 95 >99.9 <1 <1 <1 betaine TG106 NBS + 1055± 19 95 >99.9 <1 <1 <1 betaine TG107 NBS + 1135 ± 18 96 >99.9 <1 <1 <1betaine TG108 NBS + 1287 ± 15 98 >99.9 <1 <1 <1 betaine TG112 NBS  926 ±13 95 >99.9 <1 <1 <1 10% glucose + betaine TG113 NBS + 1068 ± 3295 >99.9 <1 <1 <1 betaine TG114 NBS + 1314 ± 48 98 >99.9 <1 <1 <1betaine ^(a)NBS mineral salts medium containing 12% (w/v) glucose (pH7.0) unless specified otherwise. Where indicated, 1 mM betaine was alsoadded. Bold strains produce D-(−)-lactate. Underlined strains produceL-(+)-lactate. ^(b)Yields are based on metabolized sugar assuming amaximum theoretical yield of 2 moles of lactate per mole of hexose(equal weight conversion).

TABLE 9 Lactate productivity by engineered E. coli B Volumetric^(f)Specific^(f) Lactate Cell productivity productivity Volumetric^(f) titeryield (mmol (mmol productivity Strain^(a) (mmol l⁻¹) (g l⁻¹) l⁻¹h⁻¹)g⁻¹h⁻¹) (g l⁻¹h⁻¹) SZ194 ^(b) 1228 1.70 23.3 13.7 2.10 TG103 ^(e) 10832.12 30.1 14.2 2.71 TG105 ^(e) 969 1.84 21.1 11.5 1.90 TG106 1055 1.9824.1 12.1 2.17 TG107 1135 2.21 26.7 12.1 2.40 TG108 1287 2.29 26.2 11.42.29 TG108 ^(c) 1273 2.15 26.4 12.3 2.37 TG108 ^(d) 1268 2.36 30.0 12.72.70 TG112 ^(e) 926 1.84 20.4 11.1 1.84 TG113 1068 1.90 21.3 11.2 1.92TG114 1314 2.31 32.2 13.9 2.88 TG114 ^(c) 1204 2.05 33.9 16.6 3.05 TG114^(d) 1202 2.16 36.1 16.7 3.25 ^(a)Mineral salts (NBS) containing 12%(w/v) glucose, 1 mM betaine, controlled at pH 7.0 (unless otherwisespecified). Bold strains produce D-(−)-lactate. Underlined strainsproduce L-(+)-lactate. ^(b)pH controlled at 7.5. ^(c)5% inoculum.^(d)10% inoculum. ^(e)10% glucose. ^(f)Averaged values for the mostproductive 24-h period.

TABLE 10 Chiral lactate production from glucose by bacteria, yeasts andfungi Volumetric Media, substrate and Lactate Yield Productivity IsomerOrganisms process conditions (gl⁻¹) (%) (gl⁻¹h⁻¹) and Purity ReferenceE. coli TG114 salts, 1 mM betaine 118 98 2.88 D-(−) This study batch,glucose, 120 g l⁻¹ >99.9% E. coli JP203 rich medium (LB) 62 54 1.09D-(−) Chang et al. 1999 two-stage, fed batch Not glucose, 115 g l⁻¹reported Lactobacillus yeast extract, 117 56 6.5 D-(−) Demirci et al.delbrueckii fed-batch Not 1992 mutant DP3 glucose, 210 gl⁻¹ reportedKluyveromyces rich medium (YPD), 81 81 1.5 D-(−) Rajgarhia et al.marxianus microaerobic   99% 2004 CD590 glucose, 100 g l⁻¹ E. coli TG108salts, 1 mM betaine 116 98 2.3 L-(+) This study batch, glucose, 120gl⁻¹ >99.9% E. coli JP204 rich medium (LB), two- 47 30 0.7 L-(+) Changet al. 1999 (pLS65) stage, fed-batch Not glucose, 155 g l⁻¹ reported E.coli FBR11 rich medium (LB), 73 73 2.3 L-(+) Dien et al. 2001 (pVALDH1)simple batch, glucose, Not 100 g l⁻¹ reported Kluyveromyces yeastextract and 60 55 Not reported L-(+) Bianchi et al. 2001 lactis BM3-vitamins Not 12D (pLAZ10) fed-batch, aeration reported glucose, 110 gl⁻¹ Kluyveromyces yeast extract and corn 109 55 Not reported L-(+) Porroet al. 1999 lactis PMI/C1 steep liquor, fed-batch Not (pEPL2) withaeration, reported glucose, 200 g l⁻¹ Saccharomycesvitamin-supplemented, 12 67 Not reported L-(+) Van Maris et al.cerevisiae two-stage Not 2004b RWB850-2 glucose, 18 g l⁻¹ reportedSaccharomyces yeast extract, 122 61 Not reported L-(+) Saitoh et al.2005 cerevisiae cane juice  99.9% OC2T T165R sugars, 200 gl⁻¹Saccharomyces vitamin-supplement, 61 82 Not reported L-(+) Liu et al.2005 cerevisiae simple batch Not RWB876 glucose, 74 gl⁻¹ reportedLactabacillus yeast extract 75 92 3.2 L-(+) Kyla-Nikkila et al.helveticus simple batch Not 2000 GRL89 lactose, 81 g l⁻¹ reportedLactabacillus yeast extract 103 79 Not reported L-(+) Eddington et al.sp. NRRL B- simple batch   100% 2004 30574 glucose, 130 g l⁻¹ Rhizopusurea and rich medium 109 89 1.3 L-(+) Liaw 2003 oryzae air-lift batchNot ADM 34.31 glucose, 120 g l⁻¹ reported

TABLE 11 E. coli strains, plasmids and primers used in this studyRelevant Characteristics Sources Plasmid or Strain TG114ΔfocA-pflB::FRT, ΔadhE::FRT, ΔackA::FRT, Grabar, et al. frdA::E.chrysanthemi celY, ΔfrdBC::FRT, 2006 lacA:K. oxytoca cas AB, ΔmgsA::FRTTG117 TG114, ΔfrdBC::FRT-cat-sacB-FRT This study TG118 ΔfocA-pflB::FRT,ΔadhE::FRT, ΔackA::FRT, This study ΔfrdBC, lacA:K. oxytoca cas AB,ΔmgsA::FRT TG119 TG118, ΔackA::FRT-cat-sacB-FRT This study TG120ΔfocA-pflB::FRT, ΔadhE::FRT, ΔackA, This study ΔfrdBC, lacA:K. oxytocacas AB, ΔmgsA::FRT TG121 TG120, ΔlacZ-cynX(lacZ′-sacB-cat-cynX′) Thisstudy TG122 ΔfocA-pflB::FRT, ΔadhE::FRT, ΔackA, This study ΔfrdBC,ΔmgsA::FRT TG123 TG122, ΔmgsA::FRT-cat-sacB-FRT This study TG124ΔfocA-pflB::FRT, ΔadhE::FRT, ΔackA, This study ΔAfrdBC, ΔmgsA TG125TG124, ΔfocA-pflB:FRT-cat-sacB-FRT This study TG126 ΔfocA-pflB,ΔadhE::FRT, ΔackA, ΔfrdBC, This study ΔmgsA TG127 TG126,ΔadhE::FRT-cat-sacB-FRT This study TG128 ΔfocA-pflB, ΔadhE, ΔackA,ΔfrdBC, ΔmgsA This study TG129 TG128, improved growth at 39° C. Thisstudy TG130 TG129, improved growth at 43° C. This study Plasmids pKD46bla γ β exo (Red recombinase), temperature Datsenko and conditionalpSC101 replicon Wanner (2000) pFT-A bla flp temperature conditionalpSC101 Posfai et al. replicon (1997) pEL04 cat sacB Lee et al. (2001);Ausubel et al. (2005 pLOI4151 FRT cat sacB This study PLOI3956‘lacZ’ lacY lacA cynX′ TOPO cloned This study PLOI3957 ‘lacZ’ sacB catcynX′ This study pLOI4411 ‘frdA frdB frdC frdD’ TOPO cloned This studypLOI4412 ‘ackA’ TOPO cloned This study pLOI4413 ychE′ adhE ychG′ TOPOcloned This study pLOI4415 focA-pflB TOPO cloned This study pLOI4416‘yccT mgsA’ helD TOPO cloned This study pLOI4417 pLOI4411, ΔfrdBC Thisstudy pLOI4418 pLOI4412, ΔackA This study pLOI4419 pLOI4413, ΔadhE Thisstudy pLOI4421 pLOI4415, ΔfocA-pflB This study pLOI4422 pLOI4416, ΔmgsAThis study Primers Sense primer for tgtgctgcaaggcgattaag This studyamplification of (SEQ ID NO: 9) FRT-cat-sacB Antisense primer forttcgatcacggcacgatcat This study amplification of (SEQ ID NO: 10)FRT-cat-sacB Sense primer for ttagctagcatgtgacggaag This studyamplification of cat- (SEQ ID NO: 11) sacB with 5′ NheI site Antisenseprimer for ccgctagcatcaaagggaaaa This study amplification of cat- (SEQID NO: 12) sacB with 5′ NheI site Sense primer forctggagtacagcgacgtgaagat This study cloning frdABCD (SEQ ID NO: 13)Antisense primer for cagaacgcgctcgtagctca This study cloning frdABCD(SEQ ID NO: 14) Sense primer for gaactgcggtagttcttcactg This studycloning ackA (SEQ ID NO: 15) Antisense primer for gcgtcttgcgcgataaccagThis study cloning ackA (SEQ ID NO: 16) Sense primer forgaagtgaccagcgaatacct This study cloning lacZ-cynX (SEQ ID NO: 17)Antisense primer for ggtgatgccttcggtgatta This study cloning lacZ-cynX(SEQ ID NO: 18) Sense primer for gctattccaccgcagtctca This study cloningmgsA (SEQ ID NO: 19) Antisense primer for ttatggaagaggcgctactgc Thisstudy cloning mgsA (SEQ ID NO: 20) Sense primer for agatcgccagccgctgcaatThis study cloning focA-pflB (SEQ ID NO: 21) Antisense primer foraaccgttggtgtccagacag This study cloning focA-pflB (SEQ ID NO: 22) Senseprimer for ccgctgtctgataactggtc This study cloning adhE (SEQ ID NO: 23)Antisense primer for gcataagcggatggtcactg This study cloning adhE (SEQID NO: 24) Sense primer for P-gtggttgccaccatcgtaat This study deletingfrdBC (SEQ ID NO: 25) Antisense primer for P-cgccttctccttcttattgg Thisstudy deleting frdBC (SEQ ID NO: 26) Sense primer forP-ctggacgctgttgtattcactg This study deleting ackA (SEQ ID NO: 27)Antisense primer for P-gttgagcgcttcgctgtgag This study deleting ackA(SEQ ID NO: 28) lacZ antisense acgctagctctgacaatggca This study primerwith 5′ NheI (SEQ ID NO: 29) site cynX antisense acgctagcattgccgctgataThis study primer with 5′ NheI (SEQ ID NO: 30) site Sense primer forP-agcgttatctcgcggaccgt This study deleting mgsA (SEQ ID NO: 31)Antisense primer for P-aagtgcgagtcgtcagttcc This study deleting mgsA(SEQ ID NO: 32) Sense primer for P-gcagcaggacgttattactc This studydeleting focA-pflB (SEQ ID NO: 33) Antisense primer forP-gcctacattgcgtaggctatt This study deleting focA-pflB (SEQ ID NO: 34)Sense primer for P-gctgctccggctaaagctga This study deleting adhE (SEQ IDNO: 35) Antisense primer for P-acgctctacgagtgcgttaag This study deletingadhE (SEQ ID NO: 36)

TABLE 12 Partial Sequence of Region of Deletions Foreign Strain/ DNAgene Partial Sequence ^(a) (bp) TG114 GCCAATAACAAGGAGAAGGCG AATGGATCTGATAGATTGTTTTTAAAAAATTGTTTTTGG 322 frdABCCTCTCGACAATTTCCAACAACATCCCTATATTTATCCCATCTAAAAGGCCTCTACCTTGAAAAGGCGAGGCTACCTGCTTGTTTTTCGGGACAGGATCCTCTAGAGTCAACCTGCTTGTTACTCGTGATCCCATTCACAAGGGCGAATTAATTCCCCCTTCTGTTCCGTTACCAACACTGAGCCGGACAGTAATGGGAAAGCCAAGTGTAGGCTGGAGCTGCTTCGAAGTTCCTATACTTTCTAGAGAATAGGAACTTCGGAATAGGAACTAAGGAGGATATTCATATG GTGGTTGCCACCATCGTAATCCTGTT ^(b) (SEQ ID NO: 37) TG128GCCAATAAGAAGGAGAAGGCG-GTGGTTGCCACCATCGTAATCCTGTT ^(c) 0 frdABC (SEQ IDNO: 38) TG114 CTCACAGCGAAGCGCTCAACTTTATCGTTAATACTATTCTGGCACAAAAACCAGAACTGT 94 ackACTGCGCAGCTGACTGCTATCGGTCACCGTATCGTACACGGCGGCGAAAAGTATACCAGCTCCGTAGTGATCGATGAGTCTGTTATTCAGGGTATCAAAGATGCAGCTTCTTTTGCACCGCTGCACAACCCGGCTCACCTGATCGGTATCGAAGAAGCTCTGAAATCTTTCCCACAGCTGAAAGACAAAAACGTTGCTGTATTTGACACCGCGTTCCACCAGACTATGCCGGAAGAGTCTTACCTCTACGCCCTGCCTTACAACCTGTACAAAGAGCACGGCATCCGTCGTTACGGCGCGCACGGCACCAGCCACTTCTATGTAACCCAGGAAGCGGCAAAAATGCTGAACAAACCGGTAGAAGAACTGAACATCATCACCTGCCACCTGGGCAACGGTGGTTCCGTTTCTGCTATCCGCAACGGTAAATGCGTTGACACCTCTATGGGCCTGACCCCGCTGGAAGGTCTGGTCATGGGTACCCCTTCTGGTGAT GGGGAGCTTGTCGACAATTCGAAGTTCCTATACTTTCTAGAGAATAGGAACTTCGGATCAATTCATCGGGCGCGGGAATTCGAGCTCGGTACCC ATCGATCCGGCGATCATCTTCCACCTGCACGACACCCTGGGCATGAGCGTTGACGCAATCAACAAACTGCTGACCAAAGAGTCTGGCCTGCTGGGTCTGACCGAAGTGACCAGCGACTGCCGCTATGTTGAAGACAACTACGCGACGAAAGAAGACGCGAAGCGCGCAATGGACGTTTACTGCCACCGCCTGGCGAAATACATCGGTCCCTACACTGCGCTGATGGATGGTCGTCTGGACGCTGTTGTATTC (SEQ ID NO:39) TG128 CTCACAGCGAAGCGCTCAA-CTGGACGCTGTTGTATTC 0 ackA (SEQ ID NO: 40)TG114 ATGGAACTGACGACTCGCACTT TACCTGCGCGGAAACATAT GTGTAGGCTGGAGCTGCTT 85mgsA CGAAGTTCCTATACTTTCTAGAGAATAGGAACTTCGGAATAGGAACTAAGGAGGATATTC ATATGATATTCTGATCCCCGATTATC AGCGTTATCTCGCGGACCGTCTGA (SEQ ID NO: 41) TG128ATGGAACTGACGACTCGCACTT-AGCGTTATCTCGCGGACCGTCTGA 0 mgsA (SEQ ID NO: 42)TG114 ATAGCCTACGCAATGTAGGCTTAATGATTAGTCTGAGTTATATTACGGGGCGTTTTTTTA 85focA- ATGCCCCGCTTTACATATATTTGCATTAATAAAATAATTGTAATTATAAGGTTAAATATC pflBGGTAATTTGTATTTAATAAATACGATCGATATTGTTACTTTATTCGCCTGATGCTCCCTTTTAATTAACTGTTTTAGCGGAGGATGCGGAAAAAATTCAACTCATTTGTTAATTTTTAAAATTTATTTTTATTTGGATAATCAAATATTTACTCCGTATTTCCATAAAAACCATGCCAGT TACGGGCCTA

GAACTTCGGAATAGGAACTAAGGAGGATATTCATAT GAGAACAGCAGCAGGACGTTAT (SEQ ID NO:43) TG128 ATAGCCTACGCAATGTAGGC-GCAGCAGGACGTTAT 0 focA- (SEQ ID NO: 44)pflB TG114 AACGCACTCGTAGAGCGT GTGTAGGCTGGAGCTGCTTCGAAGTTCCTATACTTTCTAGAG84 adhE AATAGGAACTTCGGAATAGGAACTAAGGAGGATATTCATATG GCTGCTCCGGCTAAAGCT(SEQ ID NO: 45) TG128 AACGCACTCGTAGAGCGT-GCTGCTCCGGCTAAAGCT 0 adhE (SEQID NO: 46) ^(a) Shown in bold are partial sequences of the 5′ and3′region of the gene(s), in italics is the FRT scar and underlined isthe region deleted in strain TG128. ^(b) This region also containedpartial sequence from a Z. mobilis promoter as well as partial sequencefrom E. chrysanthemi celY gene (shown in underlined regular type). ^(c)The dash indicates the region of the deletion.

TABLE 13 Products from glucose fermentations Lactate Co-products (mmoll⁻¹) Strain Conditions^(a) mmol l⁻¹ Yield (%)^(b) Chiral Purity (%)Succinate Acetate Ethanol TG114 AM1, 37° C. 1314 ± 48 98 >99.9 <1 <1 <1TG128 AM1, 37° C. 1157 ± 37 96 >99.9 <1 <1 <1 TG128 AM1, 39° C.  865 ±12 95 >99.9 <1 <1 <1 TG128 AM1, 43° C.  343 ± 68 95 >99.9 <1 <1 <1 TG129AM1, 39° C. 1063 ± 26 96 >99.9 <1 <1 <1 TG129 AM1, 43° C.  934 ± 1894 >99.9 <1 <1 <1 TG130 AM1, 43° C. 1149 ± 49 97 >99.9 <1 <1 <1^(a)Mineral salts (NBS) containing 12% (w/v) glucose, 1 mM betaine,controlled at pH 7.0. ^(b)Yield are based on metabolized sugar assuminga maximum theoretical yield of 2 moles of lactate per mole of hexose(equal weight conversion).

All patents, patent applications, and publications referred to or citedherein are incorporated by reference in their entirety, including allfigures and tables, to the extent they are not inconsistent with theexplicit teachings of this specification.

It should be understood that the examples and embodiments describedherein are for illustrative purposes only and that various modificationsor changes in light thereof will be suggested to persons skilled in theart and are to be included within the spirit and purview of thisapplication.

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1. A composition of matter comprising: (a) a genetically modified E.coli strain that comprises the following genetic modifications to E.coli strain KO11 (ATCC 55124): a) insertion of the Klebsiella oxytocacasAB gene behind the stop codon of lacY; b) integration of the Erwiniachrysanthemi celY gene into the frdA gene; c) inactivation or deletionof focA-Z. mobilis pdc-adhB-pflB; d) inactivation or deletion of thenative E. coli alcohol dehydrogenase gene; and e) inactivation ordeletion of the acetate kinase (ackA) gene; (b) a genetically modifiedE. coli strain that comprises the following genetic modifications to E.coli strain KO11 (ATCC 55124): a) insertion of the Klebsiella oxytocacasAB gene behind the stop codon of lacY; b) integration of the Erwiniachrysanthemi celY gene into the frdA gene; c) inactivation or deletionof focA-Z. mobilis pdc-adhB-pflB; d) inactivation or deletion of thenative E. coli alcohol dehydrogenase gene; and e) inactivation ordeletion of the acetate kinase (ackA) gene, wherein said geneticallymodified E. coli strain further comprises inactivated or deletedantibiotic resistance genes; (c) a genetically modified E. coli strainthat comprises the following genetic modifications to E. coli strainKO11 (ATCC 55124): a) insertion of the Klebsiella oxytoca casAB genebehind the stop codon of lacY; b) integration of the Erwiniachrysanthemi celY gene into the frdA gene; c) inactivation or deletionof focA-Z. mobilis pdc-adhB-pflB; d) inactivation or deletion of thenative E. coli alcohol dehydrogenase gene; and e) inactivation ordeletion of the acetate kinase (ackA) gene, wherein the Klebsiellaoxytoca casAB gene and the Erwinia chrysanthemi celY gene areinactivated or deleted in said genetically modified E. coli strain afterinsertion; (d) a genetically modified E. coli strain that comprises thefollowing genetic modifications to E. coli strain KO11 (ATCC 55124): a)insertion of the Klebsiella oxytoca casAB gene behind the stop codon oflacY; b) integration of the Erwinia chrysanthemi celY gene into the frdAgene; c) inactivation or deletion of focA-Z. mobilis pdc-adhB-pflB; d)inactivation or deletion of the native E. coli alcohol dehydrogenasegene; and e) inactivation or deletion of the acetate kinase (ackA) gene,wherein said genetically modified E. coli strain further comprisesinactivated or deleted antibiotic resistance genes, wherein theKlebsiella oxytoca casAB gene and the Erwinia chrysanthemi celY gene areinactivated or deleted in said genetically modified E. coli strain afterinsertion; (e) a genetically modified E. coli strain that comprises thefollowing genetic modifications to E. coli strain KO11 (ATCC 55124): a)insertion of the Klebsiella oxytoca casAB gene behind the stop codon oflacY; b) integration of the Erwinia chrysanthemi celY gene into the frdAgene; c) inactivation or deletion of focA-Z. mobilis pdc-adhB-pflB; d)inactivation or deletion of the native E. coli alcohol dehydrogenasegene; and e) inactivation or deletion of the acetate kinase (ackA) gene,wherein said genetically modified E. coli strain further comprisesinactivated or deleted antibiotic resistance genes and said geneticallymodified E. coli strain is metabolically evolved; (f) a geneticallymodified E. coli strain that comprises the following geneticmodifications to E. coli strain KO11 (ATCC 55124): a) insertion of theKlebsiella oxytoca casAB gene behind the stop codon of lacY; b)integration of the Erwinia chrysanthemi celY gene into the frdA gene; c)inactivation or deletion of focA-Z. mobilis pdc-adhB-pflB; d)inactivation or deletion of the native E. coli alcohol dehydrogenasegene; and e) inactivation or deletion of the acetate kinase (ackA) gene,wherein the Klebsiella oxytoca casAB gene and the Erwinia chrysanthemicelY gene are inactivated or deleted in said genetically modified E.coli strain after insertion and said genetically modified E. coli strainis metabolically evolved; (g) a genetically modified E. coli strain asset forth in (a), (b), (c), (d), (e) or (f), wherein the antibioticgenes are deleted with FLP recombinase; (h) a genetically modified E.coli strain as set forth in (a), (b), (c), (d), (e) or (f), wherein themgsA gene of said strain is inactivated or deleted in said geneticallymodified E. coli strain; (i) a genetically modified E. coli strain asset forth in (a), (b), (c), (d), (e) or (f), wherein the mgsA gene ofsaid strain is inactivated or deleted in said genetically modified E.coli strain and said genetically modified E. coli strain ismetabolically evolved; (j) a genetically modified E. coli straincomprising E. coli strain SZ194 (NRRL B30863) in which the mgsA gene hasbeen inactivated or deleted; (k) a genetically modified E. coli strainas set forth in (a), (b), (c), (d), (e) or (f), further comprising aninactivated or deleted mgsA gene, an inactivated or deleted native ldhAgene, and a recombinantly inserted heterologous gene encoding anL-specific lactate dehydrogenase; (l) a genetically modified E. colistrain comprising E. coli strain SZ194 (NRRL B30863) further comprisingan inactivated or deleted mgsA gene, an inactivated or deleted nativeldhA gene and a recombinantly inserted heterologous gene encoding anL-specific lactate dehydrogenase; (m) a genetically modified E. colistrain as set forth in (a), (b), (c), (d), (e) or (f), furthercomprising an inactivated or deleted mgsA gene, an inactivated ordeleted native ldhA gene, and a recombinantly inserted heterologous geneencoding an L-specific lactate dehydrogenase, wherein said geneticallymodified E. coli strain is metabolically evolved; (n) a geneticallymodified E. coli strain comprising E. coli strain SZ194 (NRRL B30863)further comprising an inactivated or deleted mgsA gene, an inactivatedor deleted native ldhA gene and a recombinantly inserted ldhL gene,wherein said genetically modified E. coli strain is metabolicallyevolved; (o) a genetically modified E. coli strain selected from thegroup consisting of: SZ132 (NRRL B-30861); SZ186 (NRRL B-30862); SZ194(NRRL B-30863); TG103 (NRRL B-30864); TG102 (NRRL B-30921); TG105 (NRRLB-30922); TG106 (NRRL B-30923); TG107 (NRRL B-30924); TG108 (NRRLB-30925); TG112 (NRRL B-30926); TG113 (NRRL B-30927); TG114 (NRRLB-30928); TG128 (NRRL B-30962); TG129 (NRRL B-30963); and TG130 (NRRLB-30964); (p) a genetically modified E. coli strain comprising thefollowing modifications: i) inactivation or deletion of an acetatekinase gene; ii) inactivation or deletion of a fumarate reductase gene;iii) inactivation or deletion of a pyruvate formatelyase gene; iv)inactivation or deletion of an alcohol dehydrogenase gene; v)inactivation or deletion of a methylglyoxal synthase gene; and vi)insertion of a heterologous L-specific lactate dehydrogenase (ldhL)gene; or (q) medium and: (i) a genetically modified E. coli strain thatcomprises the following genetic modifications to E. coli strain KO11(ATCC 55124): a) insertion of the Klebsiella oxytoca casAB gene behindthe stop codon of lacY; b) integration of the Erwinia chrysanthemi celYgene into the frdA gene; c) inactivation or deletion of focA-Z. mobilispdc-adhB-pflB; d) inactivation or deletion of the native E. coli alcoholdehydrogenase gene; and e) inactivation or deletion of the acetatekinase (ackA) gene; (ii) a genetically modified E. coli strain thatcomprises the following genetic modifications to E. coli strain KO11(ATCC 55124): a) insertion of the Klebsiella oxytoca casAB gene behindthe stop codon of lacY; b) integration of the Erwinia chrysanthemi celYgene into the frdA gene; c) inactivation or deletion of focA-Z. mobilispdc-adhB-pflB; d) inactivation or deletion of the native E. coli alcoholdehydrogenase gene; and e) inactivation or deletion of the acetatekinase (ackA) gene, wherein said genetically modified E. coli strainfurther comprises inactivated or deleted antibiotic resistance genes;(iii) a genetically modified E. coli strain that comprises the followinggenetic modifications to E. coli strain KO11 (ATCC 55124): a) insertionof the Klebsiella oxytoca casAB gene behind the stop codon of lacY; b)integration of the Erwinia chrysanthemi celY gene into the frdA gene; c)inactivation or deletion of focA-Z. mobilis pdc-adhB-pflB; d)inactivation or deletion of the native E. coli alcohol dehydrogenasegene; and e) inactivation or deletion of the acetate kinase (ackA) gene,wherein the Klebsiella oxytoca casAB gene and the Erwinia chrysanthemicelY gene are inactivated or deleted in said genetically modified E.coli strain after insertion; (iv) a genetically modified E. coli strainthat comprises the following genetic modifications to E. coli strainKO11 (ATCC 55124): a) insertion of the Klebsiella oxytoca casAB genebehind the stop codon of lacY; b) integration of the Erwiniachrysanthemi celY gene into the frdA gene; c) inactivation or deletionof focA-Z. mobilis pdc-adhB-pflB; d) inactivation or deletion of thenative E. coli alcohol dehydrogenase gene; and e) inactivation ordeletion of the acetate kinase (ackA) gene, wherein said geneticallymodified E. coli strain further comprises inactivated or deletedantibiotic resistance genes, wherein the Klebsiella oxytoca casAB geneand the Erwinia chrysanthemi celY gene are inactivated or deleted insaid genetically modified E. coli strain after insertion; (v) agenetically modified E. coli strain that comprises the following geneticmodifications to E. coli strain KO11 (ATCC 55124): a) insertion of theKlebsiella oxytoca casAB gene behind the stop codon of lacY; b)integration of the Erwinia chrysanthemi celY gene into the frdA gene; c)inactivation or deletion of focA-Z. mobilis pdc-adhB-pflB; d)inactivation or deletion of the native E. coli alcohol dehydrogenasegene; and e) inactivation or deletion of the acetate kinase (ackA) gene,wherein said genetically modified E. coli strain further comprisesinactivated or deleted antibiotic resistance genes and said geneticallymodified E. coli strain is metabolically evolved; (vi) a geneticallymodified E. coli strain that comprises the following geneticmodifications to E. coli strain KO11 (ATCC 55124): a) insertion of theKlebsiella oxytoca casAB gene behind the stop codon of lacY; b)integration of the Erwinia chrysanthemi celY gene into the frdA gene; c)inactivation or deletion of focA-Z. mobilis pdc-adhB-pflB; d)inactivation or deletion of the native E. coli alcohol dehydrogenasegene; and e) inactivation or deletion of the acetate kinase (ackA) gene,wherein the Klebsiella oxytoca casAB gene and the Erwinia chrysanthemicelY gene are inactivated or deleted in said genetically modified E.coli strain after insertion and said genetically modified E. coli strainis metabolically evolved; (vii) a genetically modified E. coli strain asset forth in (i), (ii), (iii), (iv), (v) or (vi), wherein the antibioticgenes are deleted with FLP recombinase; (viii) a genetically modified E.coli strain as set forth in (i), (ii), (iii), (iv), (v) or (vi), whereinthe mgsA gene of said strain is inactivated or deleted in saidgenetically modified E. coli strain; (ix) a genetically modified E. colistrain as set forth in (i), (ii), (iii), (iv), (v) or (vi), wherein themgsA gene of said strain is inactivated or deleted in said geneticallymodified E. coli strain and said genetically modified E. coli strain ismetabolically evolved; (x) a genetically modified E. coli straincomprising E. coli strain SZ194 (NRRL B30863) in which the mgsA gene hasbeen inactivated or deleted; (xi) a genetically modified E. coli strainas set forth in (i), (ii), (iii), (iv), (v) or (vi), further comprisingan inactivated or deleted mgsA gene, an inactivated or deleted nativeldhA gene, and a recombinantly inserted heterologous gene encoding anL-specific lactate dehydrogenase; (xii) a genetically modified E. colistrain comprising E. coli strain SZ194 (NRRL B30863) further comprisingan inactivated or deleted mgsA gene, an inactivated or deleted nativeldhA gene and a recombinantly inserted heterologous gene encoding anL-specific lactate dehydrogenase; (xiii) a genetically modified E. colistrain as set forth in (i), (ii), (iii), (iv), (v) or (vi), furthercomprising an inactivated or deleted mgsA gene, an inactivated ordeleted native ldhA gene, and a recombinantly inserted heterologous geneencoding an L-specific lactate dehydrogenase, wherein said geneticallymodified E. coli strain is metabolically evolved; (xiv) a geneticallymodified E. coli strain comprising E. coli strain SZ194 (NRRL B30863)further comprising an inactivated or deleted mgsA gene, an inactivatedor deleted native ldhA gene and a recombinantly inserted ldhL gene,wherein said genetically modified E. coli strain is metabolicallyevolved; (xv) a genetically modified E. coli strain selected from thegroup consisting of: SZ132 (NRRL B-30861); SZ186 (NRRL B-30862); SZ194(NRRL B-30863); TG103 (NRRL B-30864); TG102 (NRRL B-30921); TG105 (NRRLB-30922); TG106 (NRRL B-30923); TG107 (NRRL B-30924); TG108 (NRRLB-30925); TG112 (NRRL B-30926); TG113 (NRRL B-30927); TG114 (NRRLB-30928); TG128 (NRRL B-30962); TG129 (NRRL B-30963); and TG130 (NRRLB-30964); or (xvi) a genetically modified E. coli strain comprising thefollowing modifications: i) inactivation or deletion of an acetatekinase gene; ii) inactivation or deletion of a fumarate reductase gene;iii) inactivation or deletion of a pyruvate formatelyase gene; iv)inactivation or deletion of an alcohol dehydrogenase gene; v)inactivation or deletion of a methylglyoxal synthase gene; and vi)insertion of a heterologous L-specific lactate dehydrogenase (ldhL)gene.
 2. A method of culturing or growing a genetically modified E. colistrain comprising inoculating a culture medium with one or moregenetically modified E. coli strain and culturing or growing said agenetically modified E. coli strain, wherein said genetically modifiedE. coli strain is: (a) a genetically modified E. coli strain thatcomprises the following genetic modifications to E. coli strain KO11(ATCC 55124): a) insertion of the Klebsiella oxytoca casAB gene behindthe stop codon of lacY; b) integration of the Erwinia chrysanthemi celYgene into the frdA gene; c) inactivation or deletion of focA-Z. mobilispdc-adhB-pflB; d) inactivation or deletion of the native E. coli alcoholdehydrogenase gene; and e) inactivation or deletion of the acetatekinase (ackA) gene; (b) a genetically modified E. coli strain thatcomprises the following genetic modifications to E. coli strain KO11(ATCC 55124): a) insertion of the Klebsiella oxytoca casAB gene behindthe stop codon of lacY; b) integration of the Erwinia chrysanthemi celYgene into the frdA gene; c) inactivation or deletion of focA-Z. mobilispdc-adhB-pflB; d) inactivation or deletion of the native E. coli alcoholdehydrogenase gene; and e) inactivation or deletion of the acetatekinase (ackA) gene, wherein said genetically modified E. coli strainfurther comprises inactivated or deleted antibiotic resistance genes;(c) a genetically modified E. coli strain that comprises the followinggenetic modifications to E. coli strain KO11 (ATCC 55124): a) insertionof the Klebsiella oxytoca casAB gene behind the stop codon of lacY; b)integration of the Erwinia chrysanthemi celY gene into the frdA gene; c)inactivation or deletion of focA-Z. mobilis pdc-adhB-pflB; d)inactivation or deletion of the native E. coli alcohol dehydrogenasegene; and e) inactivation or deletion of the acetate kinase (ackA) gene,wherein the Klebsiella oxytoca casAB gene and the Erwinia chrysanthemicelY gene are inactivated or deleted in said genetically modified E.coli strain after insertion; (d) a genetically modified E. coli strainthat comprises the following genetic modifications to E. coli strainKO11 (ATCC 55124): a) insertion of the Klebsiella oxytoca casAB genebehind the stop codon of lacY; b) integration of the Erwiniachrysanthemi celY gene into the frdA gene; c) inactivation or deletionof focA-Z. mobilis pdc-adhB-pflB; d) inactivation or deletion of thenative E. coli alcohol dehydrogenase gene; and e) inactivation ordeletion of the acetate kinase (ackA) gene, wherein said geneticallymodified E. coli strain further comprises inactivated or deletedantibiotic resistance genes, wherein the Klebsiella oxytoca casAB geneand the Erwinia chrysanthemi celY gene are inactivated or deleted insaid genetically modified E. coli strain after insertion; (e) agenetically modified E. coli strain that comprises the following geneticmodifications to E. coli strain KO11 (ATCC 55124): a) insertion of theKlebsiella oxytoca casAB gene behind the stop codon of lacY; b)integration of the Erwinia chrysanthemi celY gene into the frdA gene; c)inactivation or deletion of focA-Z. mobilis pdc-adhB-pflB; d)inactivation or deletion of the native E. coli alcohol dehydrogenasegene; and e) inactivation or deletion of the acetate kinase (ackA) gene,wherein said genetically modified E. coli strain further comprisesinactivated or deleted antibiotic resistance genes and said geneticallymodified E. coli strain is metabolically evolved; (f) a geneticallymodified E. coli strain that comprises the following geneticmodifications to E. coli strain KO11 (ATCC 55124): a) insertion of theKlebsiella oxytoca casAB gene behind the stop codon of lacY; b)integration of the Erwinia chrysanthemi celY gene into the frdA gene; c)inactivation or deletion of focA-Z. mobilis pdc-adhB-pflB; d)inactivation or deletion of the native E. coli alcohol dehydrogenasegene; and e) inactivation or deletion of the acetate kinase (ackA) gene,wherein the Klebsiella oxytoca casAB gene and the Erwinia chrysanthemicelY gene are inactivated or deleted in said genetically modified E.coli strain after insertion and said genetically modified E. coli strainis metabolically evolved; (g) a genetically modified E. coli strain asset forth in (a), (b), (c), (d), (e) or (f), wherein the antibioticgenes are deleted with FLP recombinase; (h) a genetically modified E.coli strain as set forth in (a), (b), (c), (d), (e) or (f), wherein themgsA gene of said strain is inactivated or deleted in said geneticallymodified E. coli strain; (i) a genetically modified E. coli strain asset forth in (a), (b), (c), (d), (e) or (t), wherein the mgsA gene ofsaid strain is inactivated or deleted in said genetically modified E.coli strain and said genetically modified E. coli strain ismetabolically evolved; (j) a genetically modified E. coli straincomprising E. coli strain SZ194 (NRRL B30863) in which the mgsA gene hasbeen inactivated or deleted; (k) a genetically modified E. coli strainas set forth in (a), (b), (c), (d), (e) or (f), further comprising aninactivated or deleted mgsA gene, an inactivated or deleted native ldhAgene, and a recombinantly inserted heterologous gene encoding anL-specific lactate dehydrogenase; (l) a genetically modified E. colistrain comprising E. coli strain SZ194 (NRRL B30863) further comprisingan inactivated or deleted mgsA gene, an inactivated or deleted nativeldhA gene and a recombinantly inserted heterologous gene encoding anL-specific lactate dehydrogenase; (m) a genetically modified E. colistrain as set forth in (a), (b), (c), (d), (e) or (f), furthercomprising an inactivated or deleted mgsA gene, an inactivated ordeleted native ldhA gene, and a recombinantly inserted heterologous geneencoding an L-specific lactate dehydrogenase, wherein said geneticallymodified E. coli strain is metabolically evolved; (n) a geneticallymodified E. coli strain comprising E. coli strain SZ194 (NRRL B30863)further comprising an inactivated or deleted mgsA gene, an inactivatedor deleted native ldhA gene and a recombinantly inserted ldhL, gene,wherein said genetically modified E. coli strain is metabolicallyevolved; or (o) a genetically modified E. coli strain selected from thegroup consisting of: SZ132 (NRRL B-30861); SZ186 (NRRL B-30862); SZ194(NRRL B-30863); TG103 (NRRL B-30864); TG102 (NRRL B-30921); TG105 (NRRLB-30922); TG106 (NRRL B-30923); TG107 (NRRL B-30924); TG108 (NRRLB-30925); TG112 (NRRL B-30926); TG113 (NRRL B-30927); TG114 (NRRLB-30928); TG128 (NRRL B-30962); TG129 (NRRL B-30963); and TG130 (NRRLB-30964); or (p) a genetically modified E. coli strain comprising thefollowing modifications: i) inactivation or deletion of an acetatekinase gene; ii) inactivation or deletion of a fumarate reductase gene;iii) inactivation or deletion of a pyruvate formatelyase gene; iv)inactivation or deletion of an alcohol dehydrogenase gene; v)inactivation or deletion of a methylglyoxal synthase gene; and vi)insertion of a heterologous L-specific lactate dehydrogenase (ldhL)gene.
 3. A method of producing lactate or lactic acid comprisingculturing one or more genetically modified E. coli strain underconditions that allow for the production of lactic acid and optionallyneutralizing the lactic acid to form lactate, wherein said geneticallymodified E. coli strain is: (a) a genetically modified E. coli strainthat comprises the following genetic modifications to E. coli strainKO11 (ATCC 55124): a) insertion of the Klebsiella oxytoca casAB genebehind the stop codon of lacY; b) integration of the Erwiniachrysanthemi celY gene into the frdA gene; c) inactivation or deletionof focA-Z. mobilis pdc-adhB-pflB; d) inactivation or deletion of thenative E. coli alcohol dehydrogenase gene; and e) inactivation ordeletion of the acetate kinase (ackA) gene; (b) a genetically modifiedE. coli strain that comprises the following genetic modifications to E.coli strain KO11 (ATCC 55124): a) insertion of the Klebsiella oxytocacasAB gene behind the stop codon of lacY; b) integration of the Erwiniachrysanthemi celY gene into the frdA gene; c) inactivation or deletionof focA-Z. mobilis pdc-adhB-pflB; d) inactivation or deletion of thenative E. coli alcohol dehydrogenase gene; and e) inactivation ordeletion of the acetate kinase (ackA) gene, wherein said geneticallymodified E. coli strain further comprises inactivated or deletedantibiotic resistance genes; (c) a genetically modified E. coli strainthat comprises the following genetic modifications to E. coli strainKO11 (ATCC 55124): a) insertion of the Klebsiella oxytoca casAB genebehind the stop codon of lacY; b) integration of the Erwiniachrysanthemi celY gene into the frdA gene; c) inactivation or deletionof focA-Z. mobilis pdc-adhB-pflB; d) inactivation or deletion of thenative E. coli alcohol dehydrogenase gene; and e) inactivation ordeletion of the acetate kinase (ackA) gene, wherein the Klebsiellaoxytoca casAB gene and the Erwinia chrysanthemi celY gene areinactivated or deleted in said genetically modified E. coli strain afterinsertion; (d) a genetically modified E. coli strain that comprises thefollowing genetic modifications to E. coli strain KO11 (ATCC 55124): a)insertion of the Klebsiella oxytoca casAB gene behind the stop codon oflacY; b) integration of the Erwinia chrysanthemi celY gene into the frdAgene; c) inactivation or deletion of focA-Z. mobilis pdc-adhB-pflB; d)inactivation or deletion of the native E. coli alcohol dehydrogenasegene; and e) inactivation or deletion of the acetate kinase (ackA) gene,wherein said genetically modified E. coli strain further comprisesinactivated or deleted antibiotic resistance genes, wherein theKlebsiella oxytoca casAB gene and the Erwinia chrysanthemi celY gene areinactivated or deleted in said genetically modified E. coli strain afterinsertion; (e) a genetically modified E. coli strain that comprises thefollowing genetic modifications to E. coli strain KO11 (ATCC 55124): a)insertion of the Klebsiella oxytoca casAB gene behind the stop codon oflacY; b) integration of the Erwinia chrysanthemi celY gene into the frdAgene; c) inactivation or deletion of focA-Z. mobilis pdc-adhB-pflB; d)inactivation or deletion of the native E. coli alcohol dehydrogenasegene; and e) inactivation or deletion of the acetate kinase (ackA) gene,wherein said genetically modified E. coli strain further comprisesinactivated or deleted antibiotic resistance genes and said geneticallymodified E. coli strain is metabolically evolved; (f) a geneticallymodified E. coli strain that comprises the following geneticmodifications to E. coli strain KO11 (ATCC 55124): a) insertion of theKlebsiella oxytoca casAB gene behind the stop codon of lacY; b)integration of the Erwinia chrysanthemi celY gene into the frdA gene; c)inactivation or deletion of focA-Z. mobilis pdc-adhB-pflB; d)inactivation or deletion of the native E. coli alcohol dehydrogenasegene; and e) inactivation or deletion of the acetate kinase (ackA) gene,wherein the Klebsiella oxytoca casAB gene and the Erwinia chrysanthemicelY gene are inactivated or deleted in said genetically modified E.coli strain after insertion and said genetically modified E. coli strainis metabolically evolved; (g) a genetically modified E. coli strain asset forth in (a), (b), (c), (d), (e) or (f), wherein the antibioticgenes are deleted with FLP recombinase; (h) a genetically modified E.coli strain as set forth in (a), (b), (c), (d), (e) or (f), wherein themgsA gene of said strain is inactivated or deleted in said geneticallymodified E. coli strain; (i) a genetically modified E. coli strain asset forth in (a), (b), (c), (d), (e) or (0, wherein the mgsA gene ofsaid strain is inactivated or deleted in said genetically modified E.coli strain and said genetically modified E. coli strain ismetabolically evolved; (j) a genetically modified E. coli straincomprising E. coli strain SZ194 (NRRL B30863) in which the mgsA gene hasbeen inactivated or deleted; (k) a genetically modified E. coli strainas set forth in (a), (b), (c), (d), (e) or (f), further comprising aninactivated or deleted mgsA gene, an inactivated or deleted native ldhAgene, and a recombinantly inserted heterologous gene encoding anL-specific lactate dehydrogenase; (l) a genetically modified E. colistrain comprising E. coli strain SZ194 (NRRL B30863) further comprisingan inactivated or deleted mgsA gene, an inactivated or deleted nativeldhA gene and a recombinantly inserted heterologous gene encoding anL-specific lactate dehydrogenase; (m) a genetically modified E. colistrain as set forth in (a), (b), (c), (d), (e) or (f), furthercomprising an inactivated or deleted mgsA gene, an inactivated ordeleted native ldhA gene, and a recombinantly inserted heterologous geneencoding an L-specific lactate dehydrogenase, wherein said geneticallymodified E. coli strain is metabolically evolved; (n) a geneticallymodified E. coli strain comprising E. coli strain SZ194 (NRRL B30863)further comprising an inactivated or deleted mgsA gene, an inactivatedor deleted native ldhA gene and a recombinantly inserted ldhL gene,wherein said genetically modified E. coli strain is metabolicallyevolved; (o) a genetically modified E. coli strain selected from thegroup consisting of: SZ132 (NRRL B-30861); SZ186 (NRRL B-30862); SZ194(NRRL B-30863); TG103 (NRRL B-30864); TG102 (NRRL B-30921); TG105 (NRRLB-30922); TG106 (NRRL B-30923); TG107 (NRRL B-30924); TG108 (NRRLB-30925); TG112 (NRRL B-30926); TG113 (NRRL B-30927); TG114 (NRRLB-30928); TG128 (NRRL B-30962); TG129 (NRRL B-30963); and TG130 (NRRLB-30964); or (p) a genetically modified E. coli strain comprising thefollowing modifications: i) inactivation or deletion of an acetatekinase gene; ii) inactivation or deletion of a fumarate reductase gene;iii) inactivation or deletion of a pyruvate formatelyase gene; iv)inactivation or deletion of an alcohol dehydrogenase gene; v)inactivation or deletion of a methylglyoxal synthase gene; and vi)insertion of a heterologous L-specific lactate dehydrogenase (ldhL)gene.
 4. The method according to claim 3, wherein said method producesD-(−)-lactate or D-(−)-lactic acid and said one or more geneticallymodified E. coli is: (a) a genetically modified E. coli strain thatcomprises the following genetic modifications to E. coli strain KO11(ATCC 55124): a) insertion of the Klebsiella oxytoca casAB gene behindthe stop codon of lacY; b) integration of the Erwinia chrysanthemi celYgene into the frdA gene; c) inactivation or deletion of focA-Z. mobilispdc-adhB-pflB; d) inactivation or deletion of the native E. coli alcoholdehydrogenase gene; and e) inactivation or deletion of the acetatekinase (ackA) gene; (b) a genetically modified E. coli strain thatcomprises the following genetic modifications to E. coli strain KO11(ATCC 55124): a) insertion of the Klebsiella oxytoca casAB gene behindthe stop codon of lacY; b) integration of the Erwinia chrysanthemi celYgene into the frdA gene; c) inactivation or deletion of focA-Z. mobilispdc-adhB-pflB; d) inactivation or deletion of the native E. coli alcoholdehydrogenase gene; and e) inactivation or deletion of the acetatekinase (ackA) gene, wherein said genetically modified E. coli strainfurther comprises inactivated or deleted antibiotic resistance genes;(c) a genetically modified E. coli strain that comprises the followinggenetic modifications to E. coli strain KO11 (ATCC 55124): a) insertionof the Klebsiella oxytoca casAB gene behind the stop codon of lacY; b)integration of the Erwinia chrysanthemi celY gene into the frdA gene; c)inactivation or deletion of focA-Z. mobilis pdc-adhB-pflB; d)inactivation or deletion of the native E. coli alcohol dehydrogenasegene; and e) inactivation or deletion of the acetate kinase (ackA) gene,wherein the Klebsiella oxytoca casAB gene and the Erwinia chrysanthemicelY gene are inactivated or deleted in said genetically modified E.coli strain after insertion; (d) a genetically modified E. coli strainthat comprises the following genetic modifications to E. coli strainKO11 (ATCC 55124): a) insertion of the Klebsiella oxytoca casAB genebehind the stop codon of lacY; b) integration of the Erwiniachrysanthemi celY gene into the frdA gene; c) inactivation or deletionof focA-Z. mobilis pdc-adhB-pflB; d) inactivation or deletion of thenative E. coli alcohol dehydrogenase gene; and e) inactivation ordeletion of the acetate kinase (ackA) gene, wherein said geneticallymodified E. coli strain further comprises inactivated or deletedantibiotic resistance genes, wherein the Klebsiella oxytoca casAB geneand the Erwinia chrysanthemi celY gene are inactivated or deleted insaid genetically modified E. coli strain after insertion; (e) agenetically modified E. coli strain that comprises the following geneticmodifications to E. coli strain KO11 (ATCC 55124): a) insertion of theKlebsiella oxytoca casAB gene behind the stop codon of lacY; b)integration of the Erwinia chrysanthemi celY gene into the frdA gene; c)inactivation or deletion of focA-Z. mobilis pdc-adhB-pflB; d)inactivation or deletion of the native E. coli alcohol dehydrogenasegene; and e) inactivation or deletion of the acetate kinase (ackA) gene,wherein said genetically modified E. coli strain further comprisesinactivated or deleted antibiotic resistance genes and said geneticallymodified E. coli strain is metabolically evolved; (f) a geneticallymodified E. coli strain that comprises the following geneticmodifications to E. coli strain KO11 (ATCC 55124): a) insertion of theKlebsiella oxytoca casAB gene behind the stop codon of lacY; b)integration of the Erwinia chrysanthemi celY gene into the frdA gene; c)inactivation or deletion of focA-Z. mobilis pdc-adhB-pflB; d)inactivation or deletion of the native E. coli alcohol dehydrogenasegene; and e) inactivation or deletion of the acetate kinase (ackA) gene,wherein the Klebsiella oxytoca casAB gene and the Erwinia chrysanthemicelY gene are inactivated or deleted in said genetically modified E.coli strain after insertion and said genetically modified E. coli strainis metabolically evolved; (g) a genetically modified E. coli strain asset forth in (a), (b), (c), (d), (e) or (f), wherein the antibioticgenes are deleted with FLP recombinase; (h) a genetically modified E.coli strain as set forth in (a), (b), (c), (d), (e) or (f), wherein themgsA gene of said strain is inactivated or deleted in said geneticallymodified E. coli strain; (i) a genetically modified E. coli strain asset forth in (a), (b), (c), (d), (e) or (f), wherein the mgsA gene ofsaid strain is inactivated or deleted in said genetically modified E.coli strain and said genetically modified E. coli strain ismetabolically evolved; (j) a genetically modified E. coli straincomprising E. coli strain SZ194 (NRRL B30863) in which the mgsA gene hasbeen inactivated or deleted; or (k) a genetically modified E. colistrain selected from SZ194, TG112, TG113 or TG114.
 5. The methodaccording to claim 4, wherein said one or more genetically modified E.coli strain is selected from TG112, TG113, TG114 or SZ194.
 6. The methodaccording to claim 3, wherein said method produces L-(+)-lactate orL-(+)-acetic acid and said one or more genetically modified E. colistrain is: (a) a genetically modified E. coli strain as set forth in(a), (b), (c), (d), (e) or (f), further comprising an inactivated ordeleted mgsA gene, an inactivated or deleted native ldhA gene, and arecombinantly inserted heterologous gene encoding an L-specific lactatedehydrogenase; (b) a genetically modified E. coli strain comprising E.coli strain SZ194 (NRRL B30863) further comprising an inactivated ordeleted mgsA gene, an inactivated or deleted native ldhA gene and arecombinantly inserted heterologous gene encoding an L-specific lactatedehydrogenase; (c) a genetically modified E. coli strain as set forth in(a), (b), (c), (d), (e) or (f), further comprising an inactivated ordeleted mgsA gene, an inactivated or deleted native ldhA gene, and arecombinantly inserted heterologous gene encoding an L-specific lactatedehydrogenase, wherein said genetically modified E. coli strain ismetabolically evolved; (d) a genetically modified E. coli straincomprising E. coli strain SZ194 (NRRL B30863) further comprising aninactivated or deleted mgsA gene, an inactivated or deleted native ldhAgene and a recombinantly inserted ldhL gene, wherein said geneticallymodified E. coli strain is metabolically evolved; or (e) a geneticallymodified E. coli strain selected from TG103, TG105, TG106, TG107, orTG108; or (f) a genetically modified E. coli strain comprising thefollowing modifications: i) inactivation or deletion of an acetatekinase gene; ii) inactivation or deletion of a fumarate reductase gene;iii) inactivation or deletion of a pyruvate formatelyase gene; iv)inactivation or deletion of an alcohol dehydrogenase gene; v)inactivation or deletion of a methylglyoxal synthase gene; and vi)insertion of a heterologous L-specific lactate dehydrogenase (ldhL)gene.
 7. The method according to claim 3, wherein said geneticallymodified E. coli strain is cultured in a mineral salts medium.
 8. Themethod according to claim 4, wherein said genetically modified E. colistrain is cultured in a mineral salts medium.
 9. The method according toclaim 5, wherein said genetically modified E. coli strain is cultured ina mineral salts medium.
 10. The method according to claim 6, whereinsaid genetically modified E. coli strain is cultured in a mineral saltsmedium.
 11. The method according to claim 4, wherein said methodproduces chirally pure D-(−)-lactate or D-(−)-lactic acid.
 12. Themethod according to claim 6, wherein said method produces chirally pureL-(+)-lactate or L-(+)-lactic acid.
 13. The method according to claim 8,wherein said method produces chirally pure D-(−)-lactate or D-(−)-lacticacid.
 14. The method according to claim 10, wherein said method produceschirally pure L-(+)-lactate or L-(+)-lactic acid.
 15. The methodaccording to claim 3, further comprising the step of purifying thechirally pure lactate.
 16. The method according to claim 3, whereinlactate or lactic acid is produced at concentrations of at least 0.5M.17. The method according to claim 3, wherein the culture medium is achemically defined mineral salts medium or NBS mineral salts medium. 18.The method according to claim 3, wherein the yield of lactic acid is atleast 90%.
 19. The method according to claim 18, wherein the yield is atleast 90%, 90.5%, 91%, 91.5%, 92%, 92.5%, 93%, 93.5%, 94%, 94.5%, 95%,95.5%, 96%, 96.5%, 97%, 97.5%, 98%, 98.5%, or 99%.
 20. The methodaccording to claim 18, wherein there is no detectable contamination ofone stereoisomeric form of lactic acid or lactate with the otherstereoisomeric form or the chiral purity of the specified stereoisomeris at least 99.9%.